GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Klebsiella michiganensis M5al

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1

Query= BRENDA::P25516
         (891 letters)



>FitnessBrowser__Koxy:BWI76_RS11940
          Length = 890

 Score = 1611 bits (4171), Expect = 0.0
 Identities = 796/890 (89%), Positives = 835/890 (93%)

Query: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTE 60
           MSSTLR ASKDTLQ KDKT+HYYSLPLAAK LGD++RLPKSLKVLLENLLRWQDG+SVT 
Sbjct: 1   MSSTLRAASKDTLQVKDKTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTA 60

Query: 61  EDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120
           EDIHALAGWLK+AHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL
Sbjct: 61  EDIHALAGWLKHAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120

Query: 121 SPVDLVIDHSVTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGIC 180
           SPVDLVIDHSVTVDRFGDD+AFEENVRLEMERNHERYVFL+WG+QAFSRFSVVPPGTGIC
Sbjct: 121 SPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVFLRWGQQAFSRFSVVPPGTGIC 180

Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
           HQVNLEYLG+AVWSE Q+GEW+A+PDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240

Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
           PVSMLIPDVVGFKL+GKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR
Sbjct: 241 PVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300

Query: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIFT 360
           ATIANMSPEYGATCGFFPIDAVTLDYMRL+GRSE+QV LVE YAKAQGMWR PGDEP+FT
Sbjct: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFT 360

Query: 361 STLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQY 420
           STL LDM  VEASLAGPKRPQDRVAL DVP+AFAAS+ELEVN   KD++P+DY +NG QY
Sbjct: 361 STLALDMGTVEASLAGPKRPQDRVALGDVPQAFAASSELEVNHAQKDKRPIDYTLNGQQY 420

Query: 421 QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL 480
            LPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAV  GLK QPWVKASLAPGSKVVSDYL
Sbjct: 421 SLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYL 480

Query: 481 AKAKLTPYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRI 540
           A AKLTP+LDELGFNLVGYGCTTCIGNSGPLPDPIE AIK+ DLTVGAVLSGNRNFEGRI
Sbjct: 481 AHAKLTPWLDELGFNLVGYGCTTCIGNSGPLPDPIERAIKQGDLTVGAVLSGNRNFEGRI 540

Query: 541 HPLVKTNWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQ 600
           HPLVKTNWLASPPLVVAYALAGNMN++L  EP+G  + G PVYLKDIWPS  E+A+AVEQ
Sbjct: 541 HPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQPVYLKDIWPSGIEVAQAVEQ 600

Query: 601 VSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPAPVEDIH 660
           VSTEMFRKEYAEVFEGTAEWK I V RSDTY WQ DSTYIRLSPFFDEM   P PVEDIH
Sbjct: 601 VSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGVEPKPVEDIH 660

Query: 661 GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGT 720
           GARILAMLGDSVTTDHISPAGSIK DSPAGRYLQ  GVER DFNSYGSRRGNHEVMMRGT
Sbjct: 661 GARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGT 720

Query: 721 FANIRIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDW 780
           FANIRIRNEMVPGVEGGMTRHLPD+  ++IYDAAM YK+E TPLAVIAGKEYGSGSSRDW
Sbjct: 721 FANIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDW 780

Query: 781 AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN 840
           AAKGPRLLG+RVVIAESFERIHRSNLIGMGILPLEFPQG+TRKTLGL GEE+IDI +LQ 
Sbjct: 781 AAKGPRLLGVRVVIAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQA 840

Query: 841 LQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNML 890
           LQPG TVPVTLTRADG QEV+ CRCRIDTATELTYYQNDGILHYVIRNML
Sbjct: 841 LQPGMTVPVTLTRADGRQEVIDCRCRIDTATELTYYQNDGILHYVIRNML 890


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: 2481
Number of extensions: 100
Number of successful extensions: 1
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: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space:   718256
Effective search space used:   718256
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 BWI76_RS11940 BWI76_RS11940 (aconitate hydratase 1)
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.25304.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 1523.2   0.0          0 1523.0   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11940  BWI76_RS11940 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11940  BWI76_RS11940 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1523.0   0.0         0         0       1     876 []      18     890 .]      18     890 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1523.0 bits;  conditional E-value: 0
                               TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71 
                                             k+ +yysl+ ++++l+++s+lpksl++lle++lr++dg +++ ed++al+ w k++++d+eia++parv++
  lcl|FitnessBrowser__Koxy:BWI76_RS11940  18 KTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTAEDIHALAGWLKHAHADREIAYRPARVLM 88 
                                             578******************************************************************** PP

                               TIGR01341  72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykf 142
                                             qdftGvpavvdlaa+reavk+lg+d++k+npl+pvdlvidhsv+vd++g+++a+e+nv+le+ern+ery f
  lcl|FitnessBrowser__Koxy:BWI76_RS11940  89 QDFTGVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVF 159
                                             *********************************************************************** PP

                               TIGR01341 143 lkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGG 213
                                             l+w+++af++++vvppgtGi+hqvnleyl+++v++++++ge++a+pd+lvGtdshttminGlGvlGwGvGG
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 160 LRWGQQAFSRFSVVPPGTGICHQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGG 230
                                             *********************************************************************** PP

                               TIGR01341 214 ieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladra 284
                                             ieaeaa+lGqpvs+ +p+v+G+kl GklreG+tatdlvltvt++lrk+gvvgkfvef+G+gl++l+ladra
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 231 IEAEAAMLGQPVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRA 301
                                             *********************************************************************** PP

                               TIGR01341 285 tianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdvea 355
                                             tianm+peyGat++ffpid+vtl+y+rltgr+e++v lve+y+kaq+++++ ++ep++t+++ ld+ +vea
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 302 TIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFTSTLALDMGTVEA 372
                                             *********************************************************************** PP

                               TIGR01341 356 svaGpkrpqdrvalkevkaafkss..lesnagekglalrkeakekklegkeaelkdgavviaaitsctnts 424
                                             s+aGpkrpqdrval +v++af++s  le+n ++k+    k++ +++l+g++++l dgavviaaitsctnts
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 373 SLAGPKRPQDRVALGDVPQAFAASseLEVNHAQKD----KRPIDYTLNGQQYSLPDGAVVIAAITSCTNTS 439
                                             *********************98845777777777....******************************** PP

                               TIGR01341 425 npsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGp 495
                                             npsvl++agllakkave Glk +p+vk+slapGskvv+dyla+++l+p+l+elGfnlvGyGcttciGnsGp
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 440 NPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYLAHAKLTPWLDELGFNLVGYGCTTCIGNSGP 510
                                             *********************************************************************** PP

                               TIGR01341 496 leeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkk 566
                                             l++ +e aik++dl+v avlsGnrnfegrihplvk+n+laspplvvayalaG++++dl++ep+gt+kdG++
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 511 LPDPIERAIKQGDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQP 581
                                             *********************************************************************** PP

                               TIGR01341 567 vylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelkl 637
                                             vylkdiwps  e+a++  ++v++e+f+key+ev+eg+++w+ ++v +sd+y+w+++styir++pff+e+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 582 VYLKDIWPSGIEVAQA-VEQVSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGV 651
                                             **************95.578*************************************************** PP

                               TIGR01341 638 epeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfa 708
                                             ep+ vedi+garil++lGds+ttdhispaGsik dspa++yl+++Gver dfnsyGsrrGnhevm+rGtfa
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 652 EPKPVEDIHGARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGTFA 722
                                             *********************************************************************** PP

                               TIGR01341 709 niriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkav 779
                                             niri+n++v+g eGg+t++lpd++ +++ydaam yk+eg+pl+v+aGkeyGsGssrdwaakg++llGv++v
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 723 NIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDWAAKGPRLLGVRVV 793
                                             *********************************************************************** PP

                               TIGR01341 780 iaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveav 850
                                             iaesferihrsnl+gmG+lplef+qg +++tlgl+gee+id+++++ l+p+ +v+v+l+++dg +e+++++
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 794 IAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQALQPGMTVPVTLTRADGRQEVIDCR 864
                                             *********************************************************************** PP

                               TIGR01341 851 lridtevelayvkkgGilqyvlrkll 876
                                             +ridt++el+y++++Gil+yv+r++l
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 865 CRIDTATELTYYQNDGILHYVIRNML 890
                                             ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (890 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 9.55
//
[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