Alignments for a candidate for amaB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for amaB in Sinorhizobium meliloti 1021

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate SM_b20891 SM_b20891 dehydrogenase

Query= SwissProt::Q64057
         (539 letters)



>FitnessBrowser__Smeli:SM_b20891
          Length = 477

 Score =  236 bits (602), Expect = 1e-66
 Identities = 154/476 (32%), Positives = 242/476 (50%), Gaps = 12/476 (2%)

Query: 51  NEGVFNGSWGGRGEVITTYCPANNEPIA-RVRQASMKDYEETIGKAKKAWNIWADIPAPK 109
           ++ +  G W G G+ +    P+N + +     +AS +D +  I  AK A+  W+     +
Sbjct: 4   HQNLIAGEWVG-GDGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILE 62

Query: 110 RGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTL 169
           R  I++K  D +  +   LGRL+S E GK L EGIGE      + ++ AG +  + G  +
Sbjct: 63  RHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVV 122

Query: 170 PSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIA 229
           PS RPG  +     P G+VGIIT +NFP+A+  W  A AL  GN  ++K A      S A
Sbjct: 123 PSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWA 182

Query: 230 VTKIIAKVLEDNLLPGAICSLTCG-GADMGTAMARDERVNLLSFTGSTQVGKQVALMVQE 288
           +  I+ +      LP  + +L  G G+ +G AM     V  ++FTGST  GK+VA+   E
Sbjct: 183 IVDILHRA----GLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVE 238

Query: 289 RFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVD 348
              K  LE+GG N  +  +DADLS+ + +A+ +A  + GQRCT   R+ + E IHD  V 
Sbjct: 239 HNRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVA 298

Query: 349 RLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVM--DHPG 406
            +      + V +   P    GP+  +  ++     +   K+EG  + +GG+V+  D PG
Sbjct: 299 AMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPG 358

Query: 407 NYVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGR 466
            Y++P + T   ++  I  +E F P+  V + K+ +E     N+   GLSS I T  L  
Sbjct: 359 FYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKH 418

Query: 467 IFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTG-GGRESGSDAWKQYMRRST 521
              +   + ++ G+V VN+PT+G +    FGG K +  G RE G  A + Y    T
Sbjct: 419 ATHF--KRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKT 472


Lambda     K      H
   0.319    0.137    0.417 

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: 664
Number of extensions: 35
Number of successful extensions: 4
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: 539
Length of database: 477
Length adjustment: 34
Effective length of query: 505
Effective length of database: 443
Effective search space:   223715
Effective search space used:   223715
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
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