GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcA in Phaeobacter inhibens BS107

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>lcl|FitnessBrowser__Phaeo:GFF2274 PGA1_c23060 ribose import
           ATP-binding protein RbsA
          Length = 503

 Score =  357 bits (915), Expect = e-103
 Identities = 218/508 (42%), Positives = 308/508 (60%), Gaps = 17/508 (3%)

Query: 10  KAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGG 69
           ++P+L L  I KTFPGVRAL  V LT   GEVHALMGENGAGKSTLMK+L G +  D G 
Sbjct: 4   QSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEG- 62

Query: 70  ECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMV 128
           +  +  Q V + GP  A+  G+  I+QELSLA  LSVAENIYLG   ++R GLV   ++ 
Sbjct: 63  QIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELE 122

Query: 129 RACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 188
                 L +L   F+    V  LSIA +Q+VEIARA+  +A+ ++ DEPT  L+  E   
Sbjct: 123 AKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVV 182

Query: 189 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248
           LF +I  L+ +G+ I YISHRM EI ++ DR++VLRDG + GT++ A  ++  + +MM+G
Sbjct: 183 LFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIG 242

Query: 249 RDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELAR 308
           R L     + H +    EV L VR ++ G   +  +F++R GEV+G  GLVGAGRTE+A 
Sbjct: 243 RKLDLSRNEAHHEL--GEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAE 300

Query: 309 LVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHE 368
            +FG    T G + +      G  V + +  P  AI+ GI+ + EDRK QGL L  +  +
Sbjct: 301 TLFGLRNPTSGSIFL-----DGAEVAITS--PHDAIERGISLVPEDRKGQGLVLGMNCRD 353

Query: 369 NINLIVAARDALGLGRLNRTAARRRTTEAI-DTLGIRVAHAQVNVGALSGGNQQKVMLSR 427
           N+ L     D L  G      A     +   D L IR    +  VG LSGGNQQK+++ +
Sbjct: 354 NMTL--PQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGK 411

Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487
            L ++P VLI+DEPTRG+D+G+K+EI+ L+  LA  G A+++ISSE+PEV+ + DR++ M
Sbjct: 412 WLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAM 471

Query: 488 REGTLAGEVRPAGSAAETQERIIALATG 515
             G +   +R   S   T+E +IA  +G
Sbjct: 472 YSGRI---MRTFTSEEVTEENLIAAISG 496



 Score = 64.3 bits (155), Expect = 1e-14
 Identities = 53/219 (24%), Positives = 98/219 (44%), Gaps = 9/219 (4%)

Query: 39  GEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQEL 98
           GEV    G  GAG++ + + L G       G   +DG  V I  P  A + G++++ ++ 
Sbjct: 282 GEVVGFYGLVGAGRTEIAETLFGLRNPT-SGSIFLDGAEVAITSPHDAIERGISLVPEDR 340

Query: 99  S---LAPNLSVAENIYLGRA--LQRRGLVARGDMVRACAPTLARLGADFSPAAN--VASL 151
               L   ++  +N+ L +   L+    VA G  +        +L    +P     V +L
Sbjct: 341 KGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIR-TPGWKQLVGNL 399

Query: 152 SIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMA 211
           S   +Q + I + +     +L++DEPT  +       +  L+R L  +G A++ IS  M 
Sbjct: 400 SGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMP 459

Query: 212 EIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
           E+  +ADR+  +  G  + T     +++  L+  + G D
Sbjct: 460 EVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLD 498


Lambda     K      H
   0.320    0.136    0.382 

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: 589
Number of extensions: 28
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 540
Length of database: 503
Length adjustment: 35
Effective length of query: 505
Effective length of database: 468
Effective search space:   236340
Effective search space used:   236340
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 (21.8 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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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:

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:

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:

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, or view the source code.

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