GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate H281DRAFT_06210 H281DRAFT_06210 aconitate hydratase

Query= BRENDA::P25516
         (891 letters)



>FitnessBrowser__Burk376:H281DRAFT_06210
          Length = 898

 Score =  878 bits (2268), Expect = 0.0
 Identities = 456/887 (51%), Positives = 597/887 (67%), Gaps = 29/887 (3%)

Query: 12  TLQAKDKTYHYYSLPLA-AKSLGDITRLPKSLKVLLENLLRWQDGNSVTEEDIHALAGWL 70
           TL+       Y  L  A A+    ++ LP SL++LLEN +R + G     +D+ A+  WL
Sbjct: 13  TLETASGPLRYADLKRAEAQGFAPLSELPVSLRILLENAMR-RGG----VDDVAAIRDWL 67

Query: 71  KNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHS 130
               +DREI++ P RVLM D + VP V DLAAMR+AV++ GGD+ +VNPL PVD+V+DHS
Sbjct: 68  TRRESDREISFFPVRVLMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHS 127

Query: 131 VTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGK 190
              D  G  +AF+ N+ LE +RNHERY FLKW + AF    VVPP TGI HQVNLE+L  
Sbjct: 128 AITDHAGRSDAFDLNLALEYQRNHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAA 187

Query: 191 AVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVV 250
            V + + D      PDTLVG DSHTTM+N +GVLGWGVGGIEA AA+LGQP+SML+P V+
Sbjct: 188 GVQTVVIDDVTFVVPDTLVGMDSHTTMVNSIGVLGWGVGGIEAAAAILGQPISMLLPRVI 247

Query: 251 GFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEY 310
           G +++G+ R G+T TD+VL++T+ LR   VVG FVEF+G+GLD+LP++DRATIANM+PE 
Sbjct: 248 GCRISGRPRSGVTCTDIVLSLTEFLRGKKVVGCFVEFFGEGLDNLPVSDRATIANMAPEA 307

Query: 311 GATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWR---NPGDEPI-FTSTLELD 366
           GAT  FFP DA T++Y+  +GRS +QV + E   KAQG+WR      +E I ++  LE D
Sbjct: 308 GATMCFFPPDAATIEYLHATGRSREQVAVAEAVLKAQGIWRPEAGADEERIAYSDRLEFD 367

Query: 367 MNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQYQLPDGA 426
           ++ V  S+AGPKRPQDRV L DV   F           H+     ++ +      L +G+
Sbjct: 368 LSAVTPSMAGPKRPQDRVDLKDVSARF-----------HR-----EFGLTAEGRGLTNGS 411

Query: 427 VVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYLAKAKLT 486
           VVIAAITSCTNTSN   ++ AGL+A+     G+K + WVK SL+PGS+VV+DYL ++ L 
Sbjct: 412 VVIAAITSCTNTSNARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVVTDYLRESGLQ 471

Query: 487 PYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRIHPLVKT 546
             LD LGFNL GYGC TC G+SG L   +   I    L V  VLSGNRNFEGR HPL + 
Sbjct: 472 DDLDSLGFNLTGYGCMTCAGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHPLARA 531

Query: 547 NWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQVST-EM 605
           N+L SP LVVAYA AG +  +L +EPI  +  G PV L D+WP   +I     ++ T  M
Sbjct: 532 NFLGSPALVVAYACAGTILRDLTTEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTM 591

Query: 606 FRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPA-PVEDIHGARI 664
           F++ YA  F+G A W+ I     D + W + STYIR  P+FD   A     + +I GAR 
Sbjct: 592 FKRVYATAFQGEARWQRIAAASGDHFDWDQASTYIRRPPYFDAGFADDGFGMANIVGARA 651

Query: 665 LAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGTFANI 724
           L MLGDS+TTDHISP G I+ ++ AGR+L G GV   DFN+  SRR NH+VMMRGTFAN+
Sbjct: 652 LLMLGDSITTDHISPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANV 711

Query: 725 RIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDWAAKG 784
           R+RNEM P  EG  +RH+P  DV+ ++ AA RY+ E+ PL VIAG +YG+GSSRDWAAKG
Sbjct: 712 RLRNEMTPDREGPWSRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKG 771

Query: 785 PRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN-LQP 843
           PRLLG+R VIAESFERIHRSNL+GMGILPL+FP G TRKTLGLTGEE   I  ++  LQP
Sbjct: 772 PRLLGVRAVIAESFERIHRSNLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEGALQP 831

Query: 844 GATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNML 890
              +   ++RA+G+++ +   CR+D   E+ +Y++ G+L Y+   +L
Sbjct: 832 HQRIECEVSRANGARDSITLICRLDIPREIAWYRHGGVLQYIAAQLL 878


Lambda     K      H
   0.317    0.135    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1946
Number of extensions: 90
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 891
Length of database: 898
Length adjustment: 43
Effective length of query: 848
Effective length of database: 855
Effective search space:   725040
Effective search space used:   725040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)

Align candidate H281DRAFT_06210 H281DRAFT_06210 (aconitate hydratase)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01341.hmm
# target sequence database:        /tmp/gapView.13932.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01341  [M=876]
Accession:   TIGR01341
Description: aconitase_1: aconitate hydratase 1
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
          0 1096.5   0.0          0 1094.4   0.0    1.7  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06210  H281DRAFT_06210 aconitate hydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06210  H281DRAFT_06210 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1094.4   0.0         0         0       5     875 ..      23     877 ..      20     878 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1094.4 bits;  conditional E-value: 0
                                    TIGR01341   5 yyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparv 69 
                                                  y  lk++e +    +s+lp slrille+++r+        +dv a+ +w +   +d+ei+f p rv
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210  23 YADLKRAEAQgFAPLSELPVSLRILLENAMRRGG-----VDDVAAIRDWLTRRESDREISFFPVRV 83 
                                                  677887776646789****************864.....4799*********************** PP

                                    TIGR01341  70 vlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefer 135
                                                  ++ d + vp+v dlaa+r+av++ g+d+ ++npl+pvd+v+dhs   d+ag ++a++ n+ le++r
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210  84 LMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHSAITDHAGRSDAFDLNLALEYQR 149
                                                  ****************************************************************** PP

                                    TIGR01341 136 nkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttmi 201
                                                  n+ery+flkwa++af n++vvpp+tGivhqvnle+la  v +   d  +++ pd+lvG dshttm+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 150 NHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAAGVQTVVIDDVTFVVPDTLVGMDSHTTMV 215
                                                  ****************************************************************** PP

                                    TIGR01341 202 nGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkf 267
                                                  n +GvlGwGvGGiea aa+lGqp+s+ +p viG ++ G+ r Gvt td+vl +te+lr k vvg f
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 216 NSIGVLGWGVGGIEAAAAILGQPISMLLPRVIGCRISGRPRSGVTCTDIVLSLTEFLRGKKVVGCF 281
                                                  ****************************************************************** PP

                                    TIGR01341 268 veffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelf 333
                                                  veffGegl++l+++dratianmape Gat++ffp d+ t++yl+ tgr+ ++v + e+ lkaq+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 282 VEFFGEGLDNLPVSDRATIANMAPEAGATMCFFPPDAATIEYLHATGRSREQVAVAEAVLKAQGIW 347
                                                  ****************************************************************** PP

                                    TIGR01341 334 vd..dsee..pkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkea 395
                                                  +    ++e  + y+d +e dls v +s+aGpkrpqdrv+lk+v a f++         +++l+   
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 348 RPeaGADEerIAYSDRLEFDLSAVTPSMAGPKRPQDRVDLKDVSARFHR---------EFGLT--- 401
                                                  973322224599*********************************8865.........44443... PP

                                    TIGR01341 396 kekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvv 461
                                                         +   l++g+vviaaitsctntsn   ++gagl+a+     G+k k +vktsl+pGs+vv
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 402 ------AEGRGLTNGSVVIAAITSCTNTSNARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVV 461
                                                  ......34556899**************************************************** PP

                                    TIGR01341 462 tdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihp 527
                                                  tdyl esgl++ l+ lGfnl GyGc tc G sG+l+ ev+  i  ++l+v++vlsGnrnfegr hp
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 462 TDYLRESGLQDDLDSLGFNLTGYGCMTCAGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHP 527
                                                  ****************************************************************** PP

                                    TIGR01341 528 lvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfk 593
                                                  l +an+l sp lvvaya aGt+  dl++epi+ + dG++v l d+wp   +i+++ ++ v+  +fk
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 528 LARANFLGSPALVVAYACAGTILRDLTTEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTMFK 593
                                                  ****************************************************************** PP

                                    TIGR01341 594 keyeevtegnerwnelevtssdlyewdekstyireppffee.lklepeevedikgarillllGdsi 658
                                                  + y++ ++g++rw+++ ++s+d ++wd+ styir+pp+f+  +  +   + +i gar ll+lGdsi
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 594 RVYATAFQGEARWQRIAAASGDHFDWDQASTYIRRPPYFDAgFADDGFGMANIVGARALLMLGDSI 659
                                                  ***************************************962566677999*************** PP

                                    TIGR01341 659 ttdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgl 724
                                                  ttdhisp G i+ ++ a+++l+  Gv + dfn+  srr nh+vm+rGtfan+r++n++ + +eG+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 660 TTDHISPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANVRLRNEMTPDREGPW 725
                                                  ****************************************************************** PP

                                    TIGR01341 725 tvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrs 790
                                                  ++++p ++v+ v++aa +y++e+vpl+v+aG++yG+Gssrdwaakg++llGv+aviaesferihrs
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 726 SRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKGPRLLGVRAVIAESFERIHRS 791
                                                  ****************************************************************** PP

                                    TIGR01341 791 nlvgmGvlplefkqgedaetlgltgeetidvddie.elkpkkevtvelvkedgeketveavlridt 855
                                                  nlvgmG+lpl+f+ g++++tlgltgee   + +ie  l+p+++++ e+ +++g + +++  +r+d 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 792 NLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEgALQPHQRIECEVSRANGARDSITLICRLDI 857
                                                  *****************************999986479**************************** PP

                                    TIGR01341 856 evelayvkkgGilqyvlrkl 875
                                                  + e+a++++gG+lqy+  +l
  lcl|FitnessBrowser__Burk376:H281DRAFT_06210 858 PREIAWYRHGGVLQYIAAQL 877
                                                  ***************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (898 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.16u 0.02s 00:00:00.18 Elapsed: 00:00:00.17
# Mc/sec: 4.41
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory