Alignments for a candidate for frcA in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Rhodobacter ovatus JA234

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_097031110.1 CRO07_RS12930 ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_900207575.1:WP_097031110.1
          Length = 506

 Score =  275 bits (703), Expect = 3e-78
 Identities = 187/488 (38%), Positives = 273/488 (55%), Gaps = 16/488 (3%)

Query: 11  APLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGE 70
           AP+L L  I K F  + A   + L+   GEV AL+GENGAGK+TLM IL G Y AD  G 
Sbjct: 4   APVLRLCGITKRFGSLVANDAISLSLNRGEVVALLGENGAGKTTLMNILFGHYVAD-AGT 62

Query: 71  CHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLG-RALQRRGLVARGDMVR 129
             + GQ +    P++A   GV +++Q  +LA NL+V +NI LG R L R GL  R  + R
Sbjct: 63  VEVMGQPLPPGHPRAALAAGVGMVHQHFTLADNLTVLDNILLGTRPLWRPGL--RKAVAR 120

Query: 130 ACAPTLAR-LGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 188
           A    L++  G    P A V +LS+ +RQ VEI +A++ +ARIL++DEPT  L+  ET+ 
Sbjct: 121 ARVQALSQDFGLSVHPDARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQETEA 180

Query: 189 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248
           LF  +R   G G++I++ISH++ E+  +ADR  VLR G  VG +  A   + AL  +MVG
Sbjct: 181 LFRTLRLAVGRGLSIIFISHKLHEVMGVADRAVVLRHGRVVGEVATADTDRHALAALMVG 240

Query: 249 RDL--SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306
            ++        T G  + R   ++         ++  + DLRAG + GLAG+ G G+  L
Sbjct: 241 EEVVPPKVAPPTPGPVLLRLDDVTTAQAGTATGLRRVTLDLRAGTITGLAGVSGNGQAAL 300

Query: 307 ARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366
           + LV G      G + IA     G  VT     PR+A+ AGIA + EDR   G   D ++
Sbjct: 301 SDLVSGVIRPQAGRLHIA-----GAPVT--HWTPREAVGAGIARIPEDRHSTGTIADFTL 353

Query: 367 HENINLI-VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVML 425
            EN  L    +R A G G +N  AAR      I T  +R       +  LSGGN QK++L
Sbjct: 354 TENAILEGYRSRFAKG-GWMNWRAARAFAEGIIRTYDVRCPGPDTRIRLLSGGNMQKLIL 412

Query: 426 SRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVL 485
            R+LE  PR+++ ++P RG+DIGA + ++  +     +G A+L+IS +L E++ L D + 
Sbjct: 413 GRVLEPGPRIILANQPVRGLDIGAITYVHSRLLQARDAGAAVLLISEDLDEIMALSDSIH 472

Query: 486 VMREGTLA 493
           V+ EG L+
Sbjct: 473 VISEGRLS 480



 Score =  104 bits (259), Expect = 9e-27
 Identities = 82/267 (30%), Positives = 119/267 (44%), Gaps = 31/267 (11%)

Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQA 343
           S  L  GEV+ L G  GAG+T L  ++FG      G V +           LP G PR A
Sbjct: 26  SLSLNRGEVVALLGENGAGKTTLMNILFGHYVADAGTVEVMGQP-------LPPGHPRAA 78

Query: 344 IDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGI 403
           + AG+  +      Q   L  ++    N+++  R     G L +  AR R        G+
Sbjct: 79  LAAGVGMVH-----QHFTLADNLTVLDNILLGTRPLWRPG-LRKAVARARVQALSQDFGL 132

Query: 404 RVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQS 463
            V H    VG LS G +Q+V + + L    R+LILDEPT  +       ++R +      
Sbjct: 133 SV-HPDARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQETEALFRTLRLAVGR 191

Query: 464 GVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAPAW 523
           G++I+ IS +L EV+G+ DR +V+R G + GEV    + A+T    +A         P  
Sbjct: 192 GLSIIFISHKLHEVMGVADRAVVLRHGRVVGEV----ATADTDRHALAALMVGEEVVPPK 247

Query: 524 VDVPLPG-------------AGNATGI 537
           V  P PG             AG ATG+
Sbjct: 248 VAPPTPGPVLLRLDDVTTAQAGTATGL 274



 Score = 55.8 bits (133), Expect = 4e-12
 Identities = 59/227 (25%), Positives = 96/227 (42%), Gaps = 8/227 (3%)

Query: 29  LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARD 88
           LR+V L   AG +  L G +G G++ L  ++SG       G  HI G  V    P+ A  
Sbjct: 274 LRRVTLDLRAGTITGLAGVSGNGQAALSDLVSGVIRPQ-AGRLHIAGAPVTHWTPREAVG 332

Query: 89  LGVAVIYQE---LSLAPNLSVAENIYLG--RALQRRGLVARGDMVRACAPTLARLGADFS 143
            G+A I ++        + ++ EN  L   R+   +G        RA A  + R      
Sbjct: 333 AGIARIPEDRHSTGTIADFTLTENAILEGYRSRFAKGGWMNWRAARAFAEGIIRTYDVRC 392

Query: 144 PAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGM 201
           P  +  +  LS    Q + + R +    RI++ ++P   L       + + + Q R  G 
Sbjct: 393 PGPDTRIRLLSGGNMQKLILGRVLEPGPRIILANQPVRGLDIGAITYVHSRLLQARDAGA 452

Query: 202 AILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248
           A+L IS  + EI  L+D + V+ +G       R  ++Q  L   M G
Sbjct: 453 AVLLISEDLDEIMALSDSIHVISEGRLSPGFARGTMTQQQLGLWMAG 499


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: 636
Number of extensions: 38
Number of successful extensions: 9
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: 506
Length adjustment: 35
Effective length of query: 505
Effective length of database: 471
Effective search space:   237855
Effective search space used:   237855
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 24 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