Alignments for a candidate for aldA in Microvirga lotononidis WSM3557

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Microvirga lotononidis WSM3557

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_009764128.1 MICLODRAFT_RS22470 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

Query= reanno::Smeli:SMc02322
         (699 letters)



>NCBI__GCF_000262405.1:WP_009764128.1
          Length = 701

 Score = 1037 bits (2682), Expect = 0.0
 Identities = 514/691 (74%), Positives = 580/691 (83%), Gaps = 1/691 (0%)

Query: 10  LANLWDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWV 69
           L N WDD KAA + EP  LLYRSNLLG+DKRITNYGGGNTSAKVME DPLTGE VEVLWV
Sbjct: 11  LDNQWDDAKAAALDEPGLLLYRSNLLGADKRITNYGGGNTSAKVMETDPLTGETVEVLWV 70

Query: 70  KGSGGDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTP 129
           KGSGGDVGTIK+DGF+TLYMDKLR+LK +Y+GVE ED MVG+LPH TFNLN RAASIDTP
Sbjct: 71  KGSGGDVGTIKLDGFATLYMDKLRSLKNLYKGVEDEDRMVGFLPHATFNLNTRAASIDTP 130

Query: 130 LHAYVPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQ 189
           LH ++P  HVDHMHPDAIIAIAAS+NSRELT +IFG+EIGWLPW+RPG++LGL LE F +
Sbjct: 131 LHGFLPYKHVDHMHPDAIIAIAASRNSRELTREIFGEEIGWLPWRRPGFQLGLDLEAFAK 190

Query: 190 ENPDARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTGPA-FGGRSKPVLAA 248
            NP+A+GVVLESHGLFTW D AKE Y  T+ IIN+AI WF     G A FGG     L  
Sbjct: 191 ANPNAKGVVLESHGLFTWADDAKECYALTLRIINQAIQWFAERTAGKAAFGGAVASSLGR 250

Query: 249 ADRAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRT 308
            +R  IA +LMP IRG I   E K+GHFDD  AVL+FV S  L+PLA LGTSCPDHFLRT
Sbjct: 251 DERRRIAARLMPEIRGRIGQAERKLGHFDDQDAVLEFVNSADLKPLAQLGTSCPDHFLRT 310

Query: 309 KIRPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVP 368
           KIRPLV+DFDP  PDV   LAGL  A+  YRADY  YYE+ K  +SP MRDPN V++L+P
Sbjct: 311 KIRPLVLDFDPKSPDVDAVLAGLDAALEAYRADYTRYYEQSKHPNSPKMRDPNPVIFLIP 370

Query: 369 GVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQR 428
           GVGM++FA+DKATARI++EFYVNAINVMRGAS VS Y GLPEQEAFDIEYWLLEEAKLQR
Sbjct: 371 GVGMLSFARDKATARIASEFYVNAINVMRGASSVSEYQGLPEQEAFDIEYWLLEEAKLQR 430

Query: 429 MPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKD 488
           MP+PKSLAGR+A +TGGAGGIG+ATA RL+ EGACVVLADIDE +L     E S R+G+D
Sbjct: 431 MPRPKSLAGRVAFITGGAGGIGRATAERLVGEGACVVLADIDEESLATTVQEFSKRFGQD 490

Query: 489 FVRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILA 548
            VR V +NVTSE  V S F +A + FGG+DILVSNAG+A+SA VEDT LA+WN+N+DILA
Sbjct: 491 SVRGVRLNVTSEPDVLSSFIEASVEFGGIDILVSNAGIASSAPVEDTDLAMWNRNIDILA 550

Query: 549 TGYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGA 608
           TGYFLVSREAFR+FR QK GGNVVFV+SKNGLA+SP ASAYCTAKAAEIHLARCLALEGA
Sbjct: 551 TGYFLVSREAFRLFRRQKLGGNVVFVSSKNGLASSPNASAYCTAKAAEIHLARCLALEGA 610

Query: 609 SAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFPEDIA 668
            A IRVN VNPDAVLRGSKIWTGEW+EQRAA+ K+ VDELE HYR+RS+LKL+VFPEDIA
Sbjct: 611 EAGIRVNTVNPDAVLRGSKIWTGEWREQRAASSKLAVDELEEHYRKRSLLKLNVFPEDIA 670

Query: 669 EAIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699
           EAIYFLASD+SAKSTGNI+NVDAGNA SFTR
Sbjct: 671 EAIYFLASDLSAKSTGNIINVDAGNATSFTR 701


Lambda     K      H
   0.317    0.133    0.393 

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: 1292
Number of extensions: 31
Number of successful extensions: 2
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: 699
Length of database: 701
Length adjustment: 39
Effective length of query: 660
Effective length of database: 662
Effective search space:   436920
Effective search space used:   436920
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: 54 (25.4 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)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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