Alignments for a candidate for acnD in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_068173991.1 HTA01S_RS17335 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001592305.1:WP_068173991.1
          Length = 967

 Score =  644 bits (1661), Expect = 0.0
 Identities = 374/927 (40%), Positives = 527/927 (56%), Gaps = 101/927 (10%)

Query: 37  KLPYTSRVLAENLVRRCEPEMLT----ASLKQIIESKQEL-DFPWFPARVVCHDILGQTA 91
           +LP + R++ E+++R C+ E +T    A L Q   S     + P+  ARVV  D  G   
Sbjct: 43  RLPVSLRIVLESVLRHCDGERVTPEHVAQLAQWQPSAARTQEIPFTVARVVLQDFTGVPL 102

Query: 92  LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151
           L DLA +R      G DP ++ P+VP  L+VDHS+ V+Y G  K+A   N  +E +RN +
Sbjct: 103 LADLAAMRSVAQRLGKDPKRIEPLVPVDLVVDHSVMVDYYG-TKNALDLNMKLEFQRNRE 161

Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPHVD 211
           R+ F+ W  +AF    V+P G GI+HQ+NLE ++  +H + G+ +PDTLVGTDSHT  ++
Sbjct: 162 RYEFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHLKGGLYYPDTLVGTDSHTTMIN 221

Query: 212 ALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQK 271
            +GV+  GVGG+EAE+ MLG+  Y   PD++G ELTG+ + G TATD+VL +TE LR+ K
Sbjct: 222 GIGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGFELTGRLREGCTATDLVLTVTEILRSHK 281

Query: 272 VVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKL 331
           VV  ++EFFGEG  +L L DRATI+NM PE+GAT   F +D +TLDY   TGR   +++ 
Sbjct: 282 VVGKFVEFFGEGTASLVLPDRATIANMAPEYGATMGFFPVDDKTLDYFRGTGRSKAEIEA 341

Query: 332 VETYAKTAGLW--------SDDLKQAVYPRTLHFDLSSVVRTIAGP-------------- 369
            E Y +  GL+        S       Y + +  DL  V  ++AGP              
Sbjct: 342 FEAYFRAQGLFGVPGAAGASQAAGDIDYSQVVRLDLGLVTPSLAGPKRPQDRIELGQVAQ 401

Query: 370 ------SNPHAR------------------------------VPTSELAARGISGEVENE 393
                 S P+A+                               PT   A R ++    N+
Sbjct: 402 QFADLFSKPNAQNGFNRPAELLHTRYQPELGQPADPPAPEKATPTPAGAPRFVAEMEANK 461

Query: 394 P-------GLMP------------DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGL 434
           P       G  P            +G V+IAAITSCTNTSNP  ++AAGLLA+ A   GL
Sbjct: 462 PARAIAHAGAEPQSHAVLKKLSIGNGDVLIAAITSCTNTSNPGVLLAAGLLAKRAVEAGL 521

Query: 435 TRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEV 494
             +P +KTSLAPGS+ V  YL    LLP LE LGF + G+ CTTC G +G L P +   +
Sbjct: 522 KVQPHIKTSLAPGSRIVTEYLTATGLLPYLEKLGFSLAGYGCTTCIGNAGDLTPELNAVI 581

Query: 495 IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDG 554
              DL   AVLSGNRNF+ RIHP  K  FLASPPLVVAYAIAG +  D+  + LGL K G
Sbjct: 582 TQNDLVCAAVLSGNRNFEARIHPNLKANFLASPPLVVAYAIAGNVMKDLMTEPLGLGKGG 641

Query: 555 KPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPL----YDWRPQS 610
           KPV L ++WP   EI  ++  ++  + +R+ Y  +        +++  +    Y W P S
Sbjct: 642 KPVYLGDVWPDSDEIHKLMRFAMNGKAYRENYARVASEPGKLWERIHGVSGNAYTW-PVS 700

Query: 611 TYIRRPPYWEG---ALAGER--TLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHK 665
           +YI  PP++E    A   E+   ++G R +A+ GD+ITTDH+SP+ +I   S AG++L  
Sbjct: 701 SYIAEPPFFEHFELAQPAEQAPAVRGARVMALFGDSITTDHISPAGSIKESSPAGQWLLA 760

Query: 666 MGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAI--VDGKVKQGSLARIEPEGI--- 720
            G+ + DFNSY   RG H    R TFAN ++KN M     DG  ++G     + EG+   
Sbjct: 761 RGVLKADFNSYGARRGHHEVMMRGTFANVRIKNLMLAPGADGSREEGGWTIYQNEGVGQG 820

Query: 721 -VTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
               +++A   Y     P ++ AG +YG GSSRDWAAKG +L G+ A+VA  FERIHR+N
Sbjct: 821 QKMSIFDAAMRYQAAGVPTVVFAGEEYGTGSSRDWAAKGTQLLGIRAVVARSFERIHRSN 880

Query: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDVI--GSIAPRADLTVIITRKNGERVEVPVTC 837
           LVGMGVLPL+F+ G++    G+ G E  DV+    + P+++ T++ITR +G+R EV +T 
Sbjct: 881 LVGMGVLPLQFQPGDSWERLGLTGEEQIDVLPHPQLLPQSEATMVITRPDGQRREVALTL 940

Query: 838 RLDTAEEVSIYEAGGVLQRFAQDFLES 864
           R+DT  EV+ Y AGG+L    +  L++
Sbjct: 941 RIDTPVEVNYYRAGGILPYVLRQLLDA 967


Lambda     K      H
   0.318    0.136    0.397 

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: 2138
Number of extensions: 112
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 967
Length adjustment: 43
Effective length of query: 824
Effective length of database: 924
Effective search space:   761376
Effective search space used:   761376
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 (21.7 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources