Alignments for a candidate for acnD in Psychromonas ingrahamii 37

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Psychromonas ingrahamii 37

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_011770203.1 PING_RS09730 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000015285.1:WP_011770203.1
          Length = 868

 Score = 1394 bits (3608), Expect = 0.0
 Identities = 692/864 (80%), Positives = 754/864 (87%), Gaps = 3/864 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MN  YRKPLPGT+LDYFDTREA+  I  GAY KLPYTSRV AENLVRRC P+ L  SL Q
Sbjct: 1   MNDNYRKPLPGTSLDYFDTREAVNNIKKGAYEKLPYTSRVFAENLVRRCAPDKLVDSLNQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE KQ+LDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDPA+VNPVVPTQLIVDH
Sbjct: 61  LIERKQDLDFPWYPARVVCHDILGQTALVDLAGLRDAIALKGGDPAKVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE+ GF+KDAF  NR IEDRRN+DRFHFINWT+ AF+N++VIP GNGIMHQINLE+M
Sbjct: 121 SLAVEHAGFEKDAFELNREIEDRRNDDRFHFINWTKTAFENVEVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI +R GVAFPDTLVGTDSHTPHVDALGV+A+GVGGLEAESVMLGRASYMR+PDI+GV
Sbjct: 181 SPVIQSREGVAFPDTLVGTDSHTPHVDALGVLALGVGGLEAESVMLGRASYMRMPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
            L GK Q GITATDIVLA+TEFLR QKVVS YLEF+GEGA  LTLGDRATISNMTPEFGA
Sbjct: 241 HLFGKRQEGITATDIVLAITEFLRNQKVVSCYLEFYGEGAANLTLGDRATISNMTPEFGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           +A MFYID+ T++YL LTGR+ +QV+LVE YAK  GLW+DDL  A Y R + FDLS+V R
Sbjct: 301 SAGMFYIDKNTIEYLKLTGRDEKQVELVENYAKQTGLWADDLVNAEYERVIDFDLSAVGR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
            IAGPSNPH RV T++LAA+GISG VENE G MPDGA IIAAITSCTNTSNPRNVIAA L
Sbjct: 361 NIAGPSNPHRRVSTADLAAKGISGVVENEAGKMPDGACIIAAITSCTNTSNPRNVIAAAL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           +ARNAN  GLTRKPWVKTSLAPGSK VQLYLEEANLL ELE LGFGIVGFACTTCNGMSG
Sbjct: 421 VARNANKLGLTRKPWVKTSLAPGSKTVQLYLEEANLLTELEELGFGIVGFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDP IQ+EVI+RDLY TAVLSGNRNFDGRIHPYAKQAF+ASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPKIQEEVIERDLYTTAVLSGNRNFDGRIHPYAKQAFIASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYG---DKVS 601
            D LG+D DG  + L +IWPSDAEID +I   VKP QF+ VYEPMFD+ VDY    +K+S
Sbjct: 541 NDALGIDPDGNKITLKDIWPSDAEIDEIITQCVKPAQFKAVYEPMFDIKVDYDEELEKIS 600

Query: 602 PLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGE 661
           P+YDWRP+STYIRRPPYW GALAGERTLK MRPLAVLGDNITTDHLSPSNAIM+DSAAG 
Sbjct: 601 PVYDWRPESTYIRRPPYWSGALAGERTLKNMRPLAVLGDNITTDHLSPSNAIMLDSAAGA 660

Query: 662 YLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIV 721
           YL KMGLPE DFNSYATHRGDHLTAQRATFANPKL NEM   DG+++QGSLAR+EPEG V
Sbjct: 661 YLDKMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVKKDGEIQQGSLARVEPEGNV 720

Query: 722 TRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLV 781
            RMWEAIE YM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTNLV
Sbjct: 721 MRMWEAIEIYMARKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLV 780

Query: 782 GMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDT 841
           GMGVLP+EF   ENR TY IDGTE FDVIG   P A LT+II R +GE + V V CRLDT
Sbjct: 781 GMGVLPVEFINAENRHTYAIDGTETFDVIGKPTPGALLTLIINRPSGETINVEVKCRLDT 840

Query: 842 AEEVSIYEAGGVLQRFAQDFLESN 865
            EEVSIYEAGG+LQRFAQDF+ES+
Sbjct: 841 EEEVSIYEAGGILQRFAQDFIESS 864


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: 2179
Number of extensions: 86
Number of successful extensions: 3
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: 868
Length adjustment: 42
Effective length of query: 825
Effective length of database: 826
Effective search space:   681450
Effective search space used:   681450
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 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