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

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_1109 ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1109
          Length = 513

 Score =  263 bits (671), Expect = 2e-74
 Identities = 170/490 (34%), Positives = 271/490 (55%), Gaps = 17/490 (3%)

Query: 19  ICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRV 78
           I K +P V A   V LT   GE+HA++GENGAGKSTLMKI+ G+   D G     +GQ V
Sbjct: 3   ITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGS-VFFNGQAV 61

Query: 79  QIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARL 138
           Q+  PQ AR LG+A+++Q  SL   L+VAEN++LG  L +   +A  ++ +  +   A  
Sbjct: 62  QVRNPQEARALGIAMVFQHFSLFDTLTVAENVWLG--LDKSLTLA--EVTQRISAKAAEY 117

Query: 139 GADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRG 198
           G D  P   V +LS+ + Q VEI RA+    ++L++DEPT+ L+    ++LF ++R+L  
Sbjct: 118 GLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLAS 177

Query: 199 EGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSGFYTKT 258
           EG +ILYISH++ EI  L    TVLR G   G  + +  + A+L ++M+G +      + 
Sbjct: 178 EGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPPALEHRA 237

Query: 259 --HGQAVEREVMLSV-RDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGADA 315
              G  V R   LS+ R    G  +    F+++AGEV+G+AG+ G G+ EL   + G D 
Sbjct: 238 VQTGATVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSGEDQ 297

Query: 316 RTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVA 375
           R            +G +      GP Q    G+ ++ E+R  +G      +    NL++ 
Sbjct: 298 RAEPASIQVTGQNAGRM------GPGQRRALGLHFVPEERLGRGAVPTMGLAH--NLLLT 349

Query: 376 ARDAL-GLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPR 434
            ++A+ G G +   A ++   + I    ++         +LSGGN QK ++ R ++  P+
Sbjct: 350 RKNAVGGSGWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPK 409

Query: 435 VLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAG 494
           +LI+ +PT GVD+GA ++I   I AL  +G A+L++S EL E+  +CDR+ V+ +G L+ 
Sbjct: 410 LLIVSQPTWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSP 469

Query: 495 EVRPAGSAAE 504
            V+ A +  E
Sbjct: 470 SVQRAEATVE 479



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 68/239 (28%), Positives = 108/239 (45%), Gaps = 21/239 (8%)

Query: 282 GCSFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPR 341
           G S  +  GE+  + G  GAG++ L ++++G+     G V     A       +    P+
Sbjct: 15  GVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQA-------VQVRNPQ 67

Query: 342 QAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTL 401
           +A   GIA + +   L   F   +V EN+ L      +L L  + +  + +     +D  
Sbjct: 68  EARALGIAMVFQHFSL---FDTLTVAENVWL--GLDKSLTLAEVTQRISAKAAEYGLDID 122

Query: 402 GIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALA 461
            +R  H       LS G  Q+V + R L   P+VLILDEPT  +   A  +++ ++  LA
Sbjct: 123 PLRPVHT------LSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLA 176

Query: 462 QSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAA 520
             G +IL IS +L E+  LC    V+R G + G   P   + ET   +  L  GA   A
Sbjct: 177 SEGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNP---SEETNASLSRLMIGAEPPA 232



 Score = 66.6 bits (161), Expect = 2e-15
 Identities = 54/217 (24%), Positives = 93/217 (42%), Gaps = 6/217 (2%)

Query: 38  AGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQE 97
           AGEV  + G +G G+  L+  LSG           + GQ     GP   R LG+  + +E
Sbjct: 271 AGEVVGIAGVSGNGQKELLYALSGEDQRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEE 330

Query: 98  L---SLAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLARLGADFS-PAANVASL 151
                  P + +A N+ L R  A+   G +  G + +     + R       P +   SL
Sbjct: 331 RLGRGAVPTMGLAHNLLLTRKNAVGGSGWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSL 390

Query: 152 SIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMA 211
           S    Q   + R +    ++L++ +PT  +      ++   I  LR  G A+L +S  + 
Sbjct: 391 SGGNLQKFIVGREIDANPKLLIVSQPTWGVDVGAAAQIRGSILALRDAGCAVLVVSEELD 450

Query: 212 EIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248
           E+ E+ DR+ V+  G    ++ RA  +   + + M G
Sbjct: 451 ELFEICDRLHVVAKGRLSPSVQRAEATVERIGEWMSG 487


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: 615
Number of extensions: 29
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 540
Length of database: 513
Length adjustment: 35
Effective length of query: 505
Effective length of database: 478
Effective search space:   241390
Effective search space used:   241390
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.

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 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