Alignments for a candidate for acnD in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Calditerrivibrio nitroreducens DSM 19672

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_013451188.1 CALNI_RS05335 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000183405.1:WP_013451188.1
          Length = 877

 Score =  703 bits (1815), Expect = 0.0
 Identities = 376/851 (44%), Positives = 543/851 (63%), Gaps = 32/851 (3%)

Query: 37  KLPYTSRVLAENLVRRC-EPEMLTASLKQIIESKQE----LDFPWFPARVVCHDILGQTA 91
           KLPY+ ++L EN++R   + ++    LK I    ++    ++ P+ P RV+  D  G  A
Sbjct: 34  KLPYSIKILVENILRNLGDGQVNEKDLKNIAGWSRKQPIPIEIPYKPVRVLMQDFTGVPA 93

Query: 92  LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151
           +VDLA +RDA+   G +P ++NP+VP  LIVDHS+ V+Y G + D+  KN A+E +RNE+
Sbjct: 94  VVDLAAMRDAMLELGKNPEKINPLVPVDLIVDHSVQVDYYGTE-DSILKNVALEYKRNEE 152

Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVI----HARNGVAFPDTLVGTDSHT 207
           R+  + W QK+F N  V+P  +GI HQ+NLE ++ V+         + + DT +GTDSHT
Sbjct: 153 RYKLLKWAQKSFHNFRVVPPNSGICHQVNLEYLAKVVCIDDRKDKKLLYLDTCIGTDSHT 212

Query: 208 PHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFL 267
           P V+ +GV+  GVGG+EAE+VMLG+  YM +P++IGV+L G+   G+TATD++L +TE L
Sbjct: 213 PMVNGIGVMGWGVGGIEAEAVMLGQPYYMPIPEVIGVKLIGELNEGVTATDLILTITEKL 272

Query: 268 RAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAE 327
           R   VV  ++E+FG G + L++ DRATISNMTPEFGAT  +F ID++T++YL +T R+  
Sbjct: 273 RRYGVVDKFVEYFGPGVKTLSIPDRATISNMTPEFGATLGIFPIDRKTIEYLRMTNRD-R 331

Query: 328 QVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAAR--- 384
              ++E YAK AG++    ++  Y   L  DL+S+  +IAGPS P  R+  S++ +    
Sbjct: 332 YADILEIYAKKAGIFYTGQEKVEYTDVLEIDLNSIEPSIAGPSRPQDRISLSQVKSNLQN 391

Query: 385 -----GISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPW 439
                 +  E++  P  + DG+V+IAAITSCTNTSNP  +I AGL+ARNA  KGL  KP+
Sbjct: 392 LKTDNFVDIEIDQNPVRIKDGSVVIAAITSCTNTSNPFVIIGAGLMARNAVKKGLRVKPY 451

Query: 440 VKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDL 499
           VKTS APGSK V+ YL+++ L+P LE+LGF I  + CTTC G SG + P I++ +I  +L
Sbjct: 452 VKTSFAPGSKVVESYLKKSGLMPYLEALGFHITAYGCTTCIGNSGPVLPQIEEAIIKNNL 511

Query: 500 YATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRL 559
              AVLSGNRNF+ RIH   +  FLASP LVVAYA+AG I  D + + LG    G+ V L
Sbjct: 512 NVAAVLSGNRNFEARIHQLVRSNFLASPMLVVAYALAGKIDIDFKNEPLGYTPYGEKVML 571

Query: 560 INIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDY---GDKVSPLYDWRPQSTYIRRP 616
            ++WPS  EI  +I+ +     F++ Y  +FD  + +     KV   Y W  +STYI++P
Sbjct: 572 KDLWPSSEEIHEIISDTFTKSDFKRDYGKIFDGDLFWQKMNVKVDKTYHWHEKSTYIKKP 631

Query: 617 PYWEGALAGER---TLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDF 673
           PY++  +        +   R L +LGD+ITTDH+SP+  I  D  AG+YL   G+ E+DF
Sbjct: 632 PYFDNFMKEPGKIFDITNARILLLLGDSITTDHISPAGEIDPDYPAGKYLISKGVKEDDF 691

Query: 674 NSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMD 733
           NSY + RG+H    R TF N ++KN+M       ++GS     PE     +++A   Y  
Sbjct: 692 NSYGSRRGNHEVMIRGTFGNIRIKNKMV-----NREGSFTVKYPENEEMFIFDAAMKYQM 746

Query: 734 RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAG 793
              PL++ AG +YG GSSRDWAAKG  L G++A++AE FERIH++NLVGMG+LPL+FK G
Sbjct: 747 ENTPLVVFAGKEYGTGSSRDWAAKGTSLLGIKAVIAESFERIHKSNLVGMGILPLQFKEG 806

Query: 794 ENRATYGIDGTEVFDVIG--SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAG 851
           E+ A Y I G EV  + G  +++PR D+ + +++ +GE+ E  VT RLDT  EV  Y  G
Sbjct: 807 ESWAKYEIKGDEVVSIFGLENLSPRKDIRIELSKPDGEKREFFVTLRLDTEVEVEYYANG 866

Query: 852 GVLQRFAQDFL 862
           G+L    + FL
Sbjct: 867 GILPYVLRRFL 877


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: 1948
Number of extensions: 101
Number of successful extensions: 10
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: 867
Length of database: 877
Length adjustment: 42
Effective length of query: 825
Effective length of database: 835
Effective search space:   688875
Effective search space used:   688875
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: 56 (26.2 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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