Alignments for a candidate for aldA in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Mesorhizobium ciceri WSM1271

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate YP_004144998.1 Mesci_5941 rhamnulose-1-phosphate aldolase/alcohol dehydrogenase

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



>NCBI__GCF_000185905.1:YP_004144998.1
          Length = 700

 Score = 1115 bits (2884), Expect = 0.0
 Identities = 553/700 (79%), Positives = 609/700 (87%), Gaps = 1/700 (0%)

Query: 1   MLDKHQGARLANLWDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLT 60
           MLDK  GARLANLWD+ KA  M+ PE L+YRSN LGSDKR+TNYGGGNTS+K+ +KDPLT
Sbjct: 1   MLDKRTGARLANLWDEAKAHAMSGPELLVYRSNTLGSDKRVTNYGGGNTSSKIWQKDPLT 60

Query: 61  GEIVEVLWVKGSGGDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLN 120
           GE VEVLWVKGSGGD  +IK+DGF+TLYMDKLRALKG+YRGVE EDEMVG+LPHCTFNLN
Sbjct: 61  GEDVEVLWVKGSGGDSASIKLDGFATLYMDKLRALKGLYRGVEHEDEMVGFLPHCTFNLN 120

Query: 121 PRAASIDTPLHAYVPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYEL 180
           PRAASIDTPLHAYVPKP VDHMHPDAIIAIAA+K+S+ LT +IFGD IGWLPWKRPG+EL
Sbjct: 121 PRAASIDTPLHAYVPKPFVDHMHPDAIIAIAAAKDSKALTKEIFGDAIGWLPWKRPGFEL 180

Query: 181 GLWLEKFCQENPDARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTGPA-FG 239
           GLWLEKFC E+P A+GV+LESHGLFTWGDT +E YETTI +IN+AI WFE  + G A FG
Sbjct: 181 GLWLEKFCLEHPAAKGVILESHGLFTWGDTPRECYETTISVINQAIEWFERRSEGVAIFG 240

Query: 240 GRSKPVLAAADRAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGT 299
           G +   L A +R AIA KLMP IRGLIS    K GHFDDS AVL+FV S  L PLAALGT
Sbjct: 241 GEAVKSLDATERRAIAAKLMPRIRGLISERSHKTGHFDDSTAVLEFVNSRDLRPLAALGT 300

Query: 300 SCPDHFLRTKIRPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRD 359
           SCPDHFLRTKIRPLV++FDPA+PDV   +A L + IA YR  Y AYY+ CK  DSP +RD
Sbjct: 301 SCPDHFLRTKIRPLVIEFDPAKPDVDAVIARLADDIAEYRVGYQAYYDSCKHPDSPTIRD 360

Query: 360 PNAVVYLVPGVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYW 419
           PNAVVYL+PGVGM TFA DKATARIS EFYVNAINVMRGAS VS+YVGLP QEAFDIEYW
Sbjct: 361 PNAVVYLMPGVGMFTFAGDKATARISGEFYVNAINVMRGASTVSSYVGLPAQEAFDIEYW 420

Query: 420 LLEEAKLQRMPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQT 479
           LLE+ KLQRMPKPKSLAG+IALVTGGAGGIG+ATANRL++EGACVVLADIDETAL +A  
Sbjct: 421 LLEDLKLQRMPKPKSLAGQIALVTGGAGGIGRATANRLLREGACVVLADIDETALASAND 480

Query: 480 ELSTRYGKDFVRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLAL 539
           EL+  YG+DFVR V +NVTSE  V SGF +  + FGG+DILVSNAGLA+SA +E+TTLAL
Sbjct: 481 ELAKVYGRDFVRPVLINVTSEEQVISGFAETAVEFGGIDILVSNAGLASSAPIEETTLAL 540

Query: 540 WNKNMDILATGYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHL 599
           WNKNMDIL+TGYFLVSREAFR+FR QK GGNVVFVASKNGLAASP A+AYCTAKAAEIHL
Sbjct: 541 WNKNMDILSTGYFLVSREAFRLFRAQKIGGNVVFVASKNGLAASPNAAAYCTAKAAEIHL 600

Query: 600 ARCLALEGASAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLK 659
           ARCLALEGA AQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKM  D+LE HYR RSMLK
Sbjct: 601 ARCLALEGAEAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMSTDDLEEHYRSRSMLK 660

Query: 660 LSVFPEDIAEAIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699
            SVFPEDIAEAIYFLASDMSAKSTGNI+NVDAGNAQSFTR
Sbjct: 661 RSVFPEDIAEAIYFLASDMSAKSTGNIINVDAGNAQSFTR 700


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: 1399
Number of extensions: 41
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: 700
Length adjustment: 39
Effective length of query: 660
Effective length of database: 661
Effective search space:   436260
Effective search space used:   436260
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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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 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