Alignments for a candidate for CCNA_00435 in Methylocella silvestris BL2

GapMind for catabolism of small carbon sources

Alignments for a candidate for CCNA_00435 in Methylocella silvestris BL2

Align Amino acid transporter (characterized, see rationale)
to candidate WP_012589784.1 MSIL_RS03830 amino acid permease

Query= uniprot:A0A0H3C3Q5
         (483 letters)



>NCBI__GCF_000021745.1:WP_012589784.1
          Length = 494

 Score =  349 bits (895), Expect = e-100
 Identities = 191/492 (38%), Positives = 293/492 (59%), Gaps = 24/492 (4%)

Query: 9   SFWTRRKAIDTITAGH-----ADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGL 62
           S W+ +         H     +++  L++TLS   L++LG+G I+G GI+ LTG   A  
Sbjct: 3   SIWSTKSIASLKAEAHEAEFGSETPNLRRTLSLASLISLGIGCIIGAGIFVLTGHAAAAY 62

Query: 63  AGPGVILSFLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEY 122
           AGP + LSF++AG VCA A LCYAE+++ +P +GSAYTY+YA +GE +AW +GW L+LEY
Sbjct: 63  AGPAISLSFVLAGLVCALAGLCYAEMASTVPVAGSAYTYAYATLGEFIAWIIGWDLLLEY 122

Query: 123 TLVCAAVAVGWSAHAHGLFK--MIGFPDALLAGP-----------HQGGLINMPAVFISM 169
                 VA+GWS +     +   IG P AL   P           H G L+N PAV I +
Sbjct: 123 AFGATTVAIGWSGYVVSFLRDFHIGIPAALAGAPFAFDPASGAWTHTGALVNAPAVAIVL 182

Query: 170 AVAGLLALGTRESATVNMVLVFVKIIALIVFVVLCLPAFNLAHF-TPFMPNGFQAHVPEG 228
           A+  LL +G  ESA VN ++V +K+  ++VF++  L + + A++ T   P+G  A +P  
Sbjct: 183 ALTALLVVGVNESAKVNNIIVAIKLAIIVVFILAGLSSVSTANWVTSANPDG--AFIPPN 240

Query: 229 AA-ADAAKVGVMAAASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIV 287
           A   +    G++  A+++FFA+ GFDAVSTAA+E KNP+RD+ +GI+GS+ +CT +Y++V
Sbjct: 241 AGPGEYGWSGILRGAAVVFFAYIGFDAVSTAAQEAKNPQRDMPLGILGSLVICTVLYVLV 300

Query: 288 AAVSIGASRTEVFSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFF 347
           + V  G    +  S  + P+   ++ +    ++ +V L A++ L +V+L  + GQ+R+ +
Sbjct: 301 SIVITGIVPFDRLSVPD-PIALGVDVIGLRWLSTVVKLGAILGLSSVVLVLLLGQTRVLY 359

Query: 348 VMARDGLLPRALSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAV 407
            +ARDGLLP   +KV+ +  TP + T+ TG++ AV++G+L +  + EL + GTL+AF  V
Sbjct: 360 SIARDGLLPPIAAKVHPRFRTPYLTTIGTGLIVAVMAGVLPIGLVGELVSIGTLFAFAIV 419

Query: 408 GASVILLRLREPNRPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVY 467
            A V+ LR   P   R F  PL  IVAP G    + L L LP  T + F     IG ++Y
Sbjct: 420 CAGVLFLRYTHPQIHRPFRAPLIAIVAPLGAAAAVVLMLGLPRDTWIRFAIWLAIGLILY 479

Query: 468 LAYGMRKSVLAQ 479
             YG R S LA+
Sbjct: 480 FTYGRRHSRLAR 491


Lambda     K      H
   0.326    0.138    0.415 

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: 733
Number of extensions: 54
Number of successful extensions: 6
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: 483
Length of database: 494
Length adjustment: 34
Effective length of query: 449
Effective length of database: 460
Effective search space:   206540
Effective search space used:   206540
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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