GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Acidovorax sp. GW101-3H11

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate Ac3H11_4835 Malate synthase G (EC 2.3.3.9)

Query= reanno::psRCH2:GFF353
         (726 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4835
          Length = 754

 Score =  958 bits (2477), Expect = 0.0
 Identities = 466/733 (63%), Positives = 590/733 (80%), Gaps = 12/733 (1%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT+R  + GLQVA  L+ F+ ++ +PGTGV   AFW G D+++ DLAP+N ALLA+RD L
Sbjct: 19  MTDRTPIHGLQVATSLFRFIEDKVLPGTGVGGEAFWKGFDAIVADLAPRNIALLAERDRL 78

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q ++D WH+A  G   + VAY+SFL++IGYL+P+  D +ATT NVD+E+A  AGPQLVVP
Sbjct: 79  QTELDTWHKANPGPIQNMVAYRSFLEKIGYLVPQPADVKATTANVDDELATQAGPQLVVP 138

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           I+NAR+ALNAANARWGSLYDALYGTDAI E DGA KG GYN +RG KVIA+AR  L++ A
Sbjct: 139 ILNARYALNAANARWGSLYDALYGTDAIPETDGAEKGKGYNPVRGAKVIAFARQVLDDTA 198

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL +GSH DSTGY++EGG+LVVSL +GSTTGLK+ +Q +G+QG A+AP +VLL++NG+H 
Sbjct: 199 PLASGSHKDSTGYKVEGGQLVVSLANGSTTGLKDASQFKGYQGNAAAPSSVLLQHNGLHL 258

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           +IQID ++PIGQ+DAAGV D+++E+AL+TI+D EDS+AAVDA+DK + Y NWLG+++  L
Sbjct: 259 DIQIDRSTPIGQSDAAGVSDLVLEAALSTILDLEDSVAAVDAEDKVLGYSNWLGIIQATL 318

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAIL--DKEG- 357
            E++ KGGK ITR +N DR+YT   G GE+ LHGRSL+F+RNVGHLMTN AIL  D +G 
Sbjct: 319 TEQVAKGGKTITRGLNGDRIYTGPTG-GEVRLHGRSLMFLRNVGHLMTNPAILWTDAQGT 377

Query: 358 -NEVPEGIMDGLFTSLIAVHNLNGNTSR--KNTRTGSMYIVKPKMHGPEEVAFATELFGR 414
             E+PEGIMD + T+ IA+H+L G+ +   +N+R GS+YIVKPKMHGP EV FA ELFGR
Sbjct: 378 QREIPEGIMDAVVTTAIALHDLQGHGANGIRNSRKGSVYIVKPKMHGPAEVGFAAELFGR 437

Query: 415 VEDVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAG 474
           VE +LGLP +T+K+GIMDEERRT++NLKACI  A  RV FINTGFLDRTGDE+HT+M AG
Sbjct: 438 VEKLLGLPDSTVKLGIMDEERRTSVNLKACIAAASSRVAFINTGFLDRTGDEMHTAMHAG 497

Query: 475 PMVRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMA 534
           PMVRK  MK   WI +YE NNV VGL+CGL+GKAQIGKGMWAMPDLMA ML+QK+ HP A
Sbjct: 498 PMVRKGDMKTSAWIQSYEKNNVLVGLSCGLRGKAQIGKGMWAMPDLMAEMLKQKIAHPKA 557

Query: 535 GANTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDD-----ILTIPLAQDTNWS 589
           GANTAWVPSPT ATLHA+HYH++ V   Q+EL K +  +  D     +LT+P+A   NWS
Sbjct: 558 GANTAWVPSPTGATLHALHYHQVKVSDIQIELEKTDVNAERDNLLTGLLTVPVAAAPNWS 617

Query: 590 EEEKRNELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRH 649
           + EK+ ELDNN+QGILGY+VRWV+QGVGCSKVPDI+++ LMEDRATLRISSQH+ANW+ H
Sbjct: 618 DAEKQQELDNNAQGILGYVVRWVDQGVGCSKVPDIHNVGLMEDRATLRISSQHLANWLHH 677

Query: 650 GVVTKDQVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYT 709
           GVVT+ QV  + +RMA VVD QN GDPLY+PMA +F  S+A++AA +LV +G +QP+GYT
Sbjct: 678 GVVTEAQVRATFERMAAVVDGQNAGDPLYQPMAGNFGTSMAYKAACDLVFKGMEQPSGYT 737

Query: 710 EPVLHRRRREFKA 722
           EP+LH  R + KA
Sbjct: 738 EPLLHAWRLKLKA 750


Lambda     K      H
   0.316    0.133    0.386 

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: 1569
Number of extensions: 71
Number of successful extensions: 5
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: 726
Length of database: 754
Length adjustment: 40
Effective length of query: 686
Effective length of database: 714
Effective search space:   489804
Effective search space used:   489804
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: 55 (25.8 bits)

Align candidate Ac3H11_4835 (Malate synthase G (EC 2.3.3.9))
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

# 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/TIGR01345.hmm
# target sequence database:        /tmp/gapView.11605.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
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 1198.3   0.0          0 1198.1   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835  Malate synthase G (EC 2.3.3.9)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835  Malate synthase G (EC 2.3.3.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1198.1   0.0         0         0       6     719 ..      26     750 ..      21     752 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1198.1 bits;  conditional E-value: 0
                                        TIGR01345   6 grlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhr 67 
                                                       +lqva+ l +f+e++vlpgtgv  e+fw+gfd+iv dlap+n  lla+rd++q+ +d +h+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835  26 HGLQVATSLFRFIEDKVLPGTGVGGEAFWKGFDAIVADLAPRNIALLAERDRLQTELDTWHK 87 
                                                      689*********************************************************** PP

                                        TIGR01345  68 knkgvi.dkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaa 128
                                                       n+g+i +  ay+sfl++igylv++p  v+ +t nvd+e+a+qagpqlvvp+lnaryalnaa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835  88 ANPGPIqNMVAYRSFLEKIGYLVPQPADVKATTANVDDELATQAGPQLVVPILNARYALNAA 149
                                                      ***7761578**************************************************** PP

                                        TIGR01345 129 narwgslydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvky 190
                                                      narwgslydalyg+++ipe+dgaekgk ynp+rg kvi+far+ ld++ pl sgs++d   y
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 150 NARWGSLYDALYGTDAIPETDGAEKGKGYNPVRGAKVIAFARQVLDDTAPLASGSHKDSTGY 211
                                                      ************************************************************** PP

                                        TIGR01345 191 kivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadk 252
                                                      k+  ++l+v l +g++t lkd +qf+gy+g+aa+p+ +ll++nglh+++qid   pig++d 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 212 KVEGGQLVVSLANGSTTGLKDASQFKGYQGNAAAPSSVLLQHNGLHLDIQIDRSTPIGQSDA 273
                                                      ************************************************************** PP

                                        TIGR01345 253 akvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklne 314
                                                      a+v d+vle+a++tild+edsvaavdaedkvl+y+n+lg+ + tl e++ k g++i+r ln 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 274 AGVSDLVLEAALSTILDLEDSVAAVDAEDKVLGYSNWLGIIQATLTEQVAKGGKTITRGLNG 335
                                                      ************************************************************** PP

                                        TIGR01345 315 drsytaangeelslhgrsllfvrnvghlmtipviltde..g..eeipegildgvltsvialy 372
                                                      dr yt++ g e+ lhgrsl+f+rnvghlmt+p+il  +  g   eipegi+d+v+t++ial+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 336 DRIYTGPTGGEVRLHGRSLMFLRNVGHLMTNPAILWTDaqGtqREIPEGIMDAVVTTAIALH 397
                                                      ********************************9964431233369***************** PP

                                        TIGR01345 373 dlkvq..nklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerr 432
                                                      dl+ +  n +rnsrkgsvyivkpkmhgp ev fa +lf+r+e+llgl+  t+k+g+mdeerr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 398 DLQGHgaNGIRNSRKGSVYIVKPKMHGPAEVGFAAELFGRVEKLLGLPDSTVKLGIMDEERR 459
                                                      **97522679**************************************************** PP

                                        TIGR01345 433 tslnlkaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaa 494
                                                      ts+nlkacia +  rvafintgfldrtgde+ht+m ag+mvrk+dmk+++w+++ye+nnv+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 460 TSVNLKACIAAASSRVAFINTGFLDRTGDEMHTAMHAGPMVRKGDMKTSAWIQSYEKNNVLV 521
                                                      ************************************************************** PP

                                        TIGR01345 495 gltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvq 556
                                                      gl cglrgkaqigkgmwampdlmaeml++k+  ++agantawvpspt+atlhalhyh+v+v 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 522 GLSCGLRGKAQIGKGMWAMPDLMAEMLKQKIAHPKAGANTAWVPSPTGATLHALHYHQVKVS 583
                                                      ************************************************************** PP

                                        TIGR01345 557 kvqkeladaerraelke....iltipvaentnwseeeikeeldnnvqgilgyvvrwveqgig 614
                                                       +q el +++ +ae+++    +lt+pva + nws+ e+++eldnn+qgilgyvvrwv+qg+g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 584 DIQIELEKTDVNAERDNlltgLLTVPVAAAPNWSDAEKQQELDNNAQGILGYVVRWVDQGVG 645
                                                      *************97762222578************************************** PP

                                        TIGR01345 615 cskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayr 676
                                                      cskvpdihnv lmedratlrissqhlanwl hg+v+  qv +++erma vvd qnagd+ y+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 646 CSKVPDIHNVGLMEDRATLRISSQHLANWLHHGVVTEAQVRATFERMAAVVDGQNAGDPLYQ 707
                                                      ************************************************************** PP

                                        TIGR01345 677 pmadnleasvafkaakdlilkgtkqpsgytepilharrlefke 719
                                                      pma+n+ +s+a+kaa dl++kg++qpsgytep+lha+rl+ k+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4835 708 PMAGNFGTSMAYKAACDLVFKGMEQPSGYTEPLLHAWRLKLKA 750
                                                      ****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (754 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 11.74
//
[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