Alignments for a candidate for RR42_RS28305 in Catellicoccus marimammalium M35/04/3

GapMind for catabolism of small carbon sources

Alignments for a candidate for RR42_RS28305 in Catellicoccus marimammalium M35/04/3

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate WP_009490181.1 C683_RS03825 amino acid permease

Query= uniprot:A0A0C4YRF7
         (472 letters)



>NCBI__GCF_000313915.1:WP_009490181.1
          Length = 448

 Score =  427 bits (1098), Expect = e-124
 Identities = 210/443 (47%), Positives = 306/443 (69%), Gaps = 5/443 (1%)

Query: 16  EKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALG 75
           ++ L RGL +RH+Q+I+IGGAIG GLFL +G++IAIAGP ++L+Y I G+ +FFIMR+LG
Sbjct: 3   QEKLERGLSNRHVQLISIGGAIGTGLFLASGKSIAIAGPSVLLAYMIVGMFVFFIMRSLG 62

Query: 76  ELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQ 135
           ELLL      SF   A +++G    F TGW+YWF W+   M+++TAV +Y+ YWFP +PQ
Sbjct: 63  ELLLANLDCHSFVELAHQYLGRRWAFVTGWTYWFCWITVAMSDLTAVGMYMRYWFPHLPQ 122

Query: 136 WIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIF-FGVTPLGPTA 194
           WIPAL  L  L  +N ++V +FGE+EFW ALIK++ IVA+I +GL +IF       G  A
Sbjct: 123 WIPALLMLLFLMALNLLSVKLFGEIEFWLALIKILAIVALIGVGLYMIFTHHKLENGIVA 182

Query: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254
           SF+NL+  GGF P G  G +L+ Q+ +F++ GVEL+G+TAGE Q+PEK LP A N +  R
Sbjct: 183 SFANLYQDGGFFPHGFSGFILSFQLAVFSFTGVELVGLTAGETQDPEKTLPKAINNIPVR 242

Query: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314
           IL+FYVG+L ++MA+ PWN + P  SPFV VF  IG+  AA+I+N VV+++AAS+CNS +
Sbjct: 243 ILLFYVGSLAVIMAVQPWNIIDPTQSPFVTVFSSIGIAAAASIINFVVLSSAASACNSAL 302

Query: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374
           FST RMLY LA+   AP+ F +++    P++A+  S+ ++GI ++LNY++PE VF  ++ 
Sbjct: 303 FSTSRMLYGLAKDDNAPKTFAKLNKNSTPAMALLMSSVVVGITIVLNYVMPEGVFSLISG 362

Query: 375 ISLVGSLWTWSIIMIAHLGYRKAIA-AGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSL 433
           IS V  L+ W+II+I H+ + K      R K   FR+ GA   N L + F+  + V+ ++
Sbjct: 363 ISTVCFLFIWTIIVICHMKFLKQTKDEDRPK---FRLKGAKVINILSLIFLALIIVICAV 419

Query: 434 DPGTRVALYVAPVWFALLGIGYR 456
              TR+AL++ P+WF  L I Y+
Sbjct: 420 LESTRIALFITPIWFIALLIIYQ 442


Lambda     K      H
   0.328    0.142    0.445 

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: 630
Number of extensions: 24
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: 472
Length of database: 448
Length adjustment: 33
Effective length of query: 439
Effective length of database: 415
Effective search space:   182185
Effective search space used:   182185
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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