GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Sinorhizobium meliloti 1021

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Smeli:SM_b20503
          Length = 512

 Score =  380 bits (976), Expect = e-110
 Identities = 218/513 (42%), Positives = 319/513 (62%), Gaps = 16/513 (3%)

Query: 9   TKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG 68
           T   +L +RN+ K F  V+AL  V+     GEVHAL GENGAGKSTLM +++G      G
Sbjct: 2   TSETVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEG 61

Query: 69  GECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMV 128
            E  I+G  V+I  P  A+ LG+A+++QE++L P+ ++AEN+++    +RR  +     +
Sbjct: 62  -EVLIEGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQL 120

Query: 129 RACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 188
              A  +    A    +  V  L I+ +QLVEIA+A+  + R+L+ DEPT  L+  E   
Sbjct: 121 ERDAQAVMNRLAPIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQV 180

Query: 189 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248
           LF +IR L+  G++I+YISHRMAE+  L DRVTV RDG +V T   + ++   +V++MVG
Sbjct: 181 LFGIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVG 240

Query: 249 RDLSGFYTKTHGQAVER--EVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306
           R++S  Y      + ER  E +LSVRD+  G R +  SF+LR GE+LG+ GL+G+GRTE+
Sbjct: 241 REISQLYPDKQPSS-ERLGEPILSVRDLG-GERFRDVSFELRYGEILGVGGLIGSGRTEI 298

Query: 307 ARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366
           A  +      T+GE+R+ +         L       A  AG+ YL+EDRK  G+FLD S+
Sbjct: 299 AEGICALRPVTQGEIRLHDK-------VLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSI 351

Query: 367 HENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 426
            +NI   +  +    LG LN    R    +    LG+R+    + V +LSGGNQQKV ++
Sbjct: 352 AQNI-AALDLKALTSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIA 410

Query: 427 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 486
           + L + P+V+++DEPTRG+D+GAKSEI+RL+  LA++G+ IL+ISSELPE++GLCDRVLV
Sbjct: 411 KQLAVDPKVILMDEPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLV 470

Query: 487 MREGTLAGEVRPAGSAAETQERIIALATGAAAA 519
           +REG +AGEV        T+E I+ LA+G   A
Sbjct: 471 VREGRIAGEV---SGNEMTEEVIMRLASGIGPA 500


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: 647
Number of extensions: 31
Number of successful extensions: 7
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: 540
Length of database: 512
Length adjustment: 35
Effective length of query: 505
Effective length of database: 477
Effective search space:   240885
Effective search space used:   240885
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:

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