Alignments for a candidate for acnD in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudomonas litoralis 2SM5

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_090272412.1 BLU11_RS05430 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_900105005.1:WP_090272412.1
          Length = 911

 Score =  737 bits (1903), Expect = 0.0
 Identities = 412/919 (44%), Positives = 566/919 (61%), Gaps = 69/919 (7%)

Query: 1   MSTVMNTQYRKPLP--GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEML 58
           MS++ + Q    L   G    Y    +A E +  G   +LP + +VL ENL+R  + + +
Sbjct: 1   MSSINSLQTLSSLQVGGRTYQYHSLPKAGELL--GEINRLPVSLKVLLENLLRHEDGDTV 58

Query: 59  T-----ASLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVN 113
           T     A    +I    + +  + PARV+  D  G  A+VDLA +RDA+A  GGDP ++N
Sbjct: 59  TREDIQAMADWMINRHSDREIQYRPARVLMQDFTGVPAVVDLAAMRDAVARAGGDPQRIN 118

Query: 114 PVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGN 173
           P+ P  L++DHS+ V++ G D  AF  N A+E +RN +R+ F+ W QKAF N  V+P G 
Sbjct: 119 PLSPVDLVIDHSVMVDHFG-DAAAFQGNVAMEIQRNGERYAFLRWGQKAFNNFRVVPPGT 177

Query: 174 GIMHQINLERMSPVIHARN----GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVM 229
           GI HQ+NLE ++  + A        A+PDTLVGTDSHT  V+ LGV+  GVGG+EAE+ M
Sbjct: 178 GICHQVNLEYLAQSVWAAEVDGQSWAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAM 237

Query: 230 LGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTL 289
           LG+   M +P+++G +LTGK + G+TATD+VL +T+ LR   VV  ++EF+G+G   L L
Sbjct: 238 LGQPVSMLIPEVVGFKLTGKLREGMTATDLVLTVTQMLRKHGVVGKFVEFYGDGLADLPL 297

Query: 290 GDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQA 349
            DRATI+NM PE+GAT   F ID+ TL YL LTGR AE V+ VE Y+K  G+W +   + 
Sbjct: 298 ADRATIANMAPEYGATCGFFPIDEITLGYLRLTGRPAEVVERVEAYSKAQGMWREPGHEP 357

Query: 350 VYPRTLHFDLSSVVRTIAGPSNPHARVPTSEL---------------------------- 381
           V+  TLH D++ V  ++AGP  P  RV  S++                            
Sbjct: 358 VFTDTLHLDMNEVEPSLAGPRRPQDRVRLSDVPKAFDELLALQTSAVRDVERLEDEGGGG 417

Query: 382 -AARGISGEV----ENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTR 436
            A  G S EV    + E  ++ +GAV+IAAITSCTNTSNP  ++AAGLLAR A  +G+ R
Sbjct: 418 TAVGGPSAEVCVTIDGEEHVLKNGAVVIAAITSCTNTSNPSVMMAAGLLARKAIERGIQR 477

Query: 437 KPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVID 496
           KPWVK+SLAPGSK V  YLE A L P L+ LGF +VG+ CTTC G SG L   I   + +
Sbjct: 478 KPWVKSSLAPGSKVVTDYLERAGLTPYLDQLGFNLVGYGCTTCIGNSGPLPEPISHAISE 537

Query: 497 RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKP 556
            DL  +AVLSGNRNF+GR+H   K  +LASPPLVVAYA+AG  R D++++ LGLD+D KP
Sbjct: 538 HDLVVSAVLSGNRNFEGRVHQQVKANWLASPPLVVAYALAGDSRLDLQEEPLGLDRDNKP 597

Query: 557 VRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF-------DLSVDYGDKVSPLYDWRPQ 609
           V L ++WPS+AEI A   A V+   FR  Y  +F        ++V  GD     Y+W  Q
Sbjct: 598 VYLRDLWPSNAEI-AEAVALVEDSMFRSRYADVFTGDEHWQSIAVSGGD----TYNWDGQ 652

Query: 610 STYIRRPPYWE---GALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKM 666
           STY++ PPY+E     +   + +   R LAV GD+ITTDH+SP+  I   S AGEYL ++
Sbjct: 653 STYVQNPPYFERIDQPIEPLQPIHQARVLAVFGDSITTDHISPAGNIKSSSPAGEYLQRL 712

Query: 667 GLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWE 726
           G+  EDFNSY + RG+H    R TFAN +++N M  + G  ++G L    P      +++
Sbjct: 713 GVKPEDFNSYGSRRGNHEVMMRGTFANIRIRNRM--LGG--EEGGLTIHTPSSERMSIYD 768

Query: 727 AIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVL 786
           A   Y     PL+++AG +YG GSSRDWAAKG  L GV+A++AE FERIHR+NLVGMGVL
Sbjct: 769 AAMRYQQEGTPLVVLAGKEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVL 828

Query: 787 PLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843
           PL+F  G+N  T  +DG EV D+ G   ++ P   L +  TR NG+++E  V CR+DT+ 
Sbjct: 829 PLQFVNGQNAPTLQLDGHEVLDIPGIDDNLRPGQILKIKATRSNGQQIEFEVVCRIDTSN 888

Query: 844 EVSIYEAGGVLQRFAQDFL 862
           EV  ++AGG+L    ++ L
Sbjct: 889 EVDYFKAGGILHYVLRELL 907


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: 2001
Number of extensions: 90
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 911
Length adjustment: 43
Effective length of query: 824
Effective length of database: 868
Effective search space:   715232
Effective search space used:   715232
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 Sep 24 2021. 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