GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Acidovorax sp. GW101-3H11

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  358 bits (919), Expect = e-103
 Identities = 213/511 (41%), Positives = 316/511 (61%), Gaps = 23/511 (4%)

Query: 11  APLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGE 70
           AP+L L  I K F G+  LR V+L  Y GE+HALMG+NGAGKSTL+K+L+G   A  GG+
Sbjct: 16  APVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEAS-GGQ 74

Query: 71  CHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMV-- 128
             + GQ V  D P +A+ LG++ +YQE++L PNLSVAENI+ GR    R  +A+G  +  
Sbjct: 75  MRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGR--YPRCGIAQGFRIDW 132

Query: 129 ----RACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTH 184
               +     +AR+G        ++   +A +QLV IARA+  E+R+L++DEPT+ L   
Sbjct: 133 ATLHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDD 192

Query: 185 ETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVK 244
           E  +LF ++R+LR EG++I++++H + ++  ++DR+TVLR+G +VG      L   AL+ 
Sbjct: 193 EVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIA 252

Query: 245 MMVGRDLSGFYTK-THGQAVEREV--MLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGA 301
            M+GRDL+    +     AV+     +L    +    +++     +RAGEV+GLAGL+G+
Sbjct: 253 AMLGRDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGS 312

Query: 302 GRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLF 361
           GRTELARL+FG +   RG +RI      G +V      P  AI  G+A   E+RK  G+ 
Sbjct: 313 GRTELARLLFGLEQPDRGALRI-----DGQVVKF--ANPMDAIRHGLALCPEERKTDGIV 365

Query: 362 LDQSVHENINLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQ 420
            + SV ENI L + AR  +G+G+ L+R+         +  LGI+       +G LSGGNQ
Sbjct: 366 AELSVRENIALALQAR--MGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQ 423

Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480
           QK +L+R + I+PR+LILDEPTRG+D+ AK EI   I  LAQ+G+A+L ISSE+ EVV +
Sbjct: 424 QKAILARWMAIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRV 483

Query: 481 CDRVLVMREGTLAGEVRPAGSAAETQERIIA 511
             R++V+R+    GE+ PAGS+ +    +IA
Sbjct: 484 AHRIVVLRDRRKVGEL-PAGSSEDAVYDLIA 513


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: 678
Number of extensions: 35
Number of successful extensions: 10
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: 517
Length adjustment: 35
Effective length of query: 505
Effective length of database: 482
Effective search space:   243410
Effective search space used:   243410
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