Alignments for a candidate for frcA in Collimonas arenae Ter10

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Collimonas arenae Ter10

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_061533691.1 CAter10_RS12710 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_001584165.1:WP_061533691.1
          Length = 516

 Score =  341 bits (874), Expect = 4e-98
 Identities = 203/489 (41%), Positives = 290/489 (59%), Gaps = 13/489 (2%)

Query: 11  APLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGE 70
           AP L L  I K F GV+AL  V L  Y GEVH LMG+NGAGKSTL+K+L+G +  + G  
Sbjct: 17  APTLELNGIYKAFGGVKALSDVSLRLYPGEVHTLMGQNGAGKSTLIKVLTGVHIPEHG-T 75

Query: 71  CHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRA 130
             ++G+ V+      A+ LG++ +YQE++L PNLSVAENI++GR   + G +    M R 
Sbjct: 76  IRLNGREVRPTSTLEAQHLGISTVYQEVNLCPNLSVAENIFIGRYPTKFGAIDWKTMQRQ 135

Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
               L  L  D    A ++   +A +Q+V I+RA+   A++L++DEPT+ L   E   LF
Sbjct: 136 AQRLLGDLQIDIDVTAPLSRYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQLLF 195

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
           +++R+LR +GMAIL+++H + +  +++DR+TVLR+G   G      L++  LV  MVG  
Sbjct: 196 SVLRKLREQGMAILFVTHFLEQTYDISDRITVLRNGVLEGEYRVDELTRLELVNKMVGSQ 255

Query: 251 LSGFY---TKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307
           +           G     E++L  R +     +     DLRAGEV GL GL+G+GRTE A
Sbjct: 256 MQSEVQAPDAATGLRDNAEIVLQARGLGRKGILAPLDLDLRAGEVYGLCGLLGSGRTETA 315

Query: 308 RLVFGADARTRGEVRIAN-PAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366
           RL+FGAD    G + I + P G         G PR+AI AGI + +EDRK +G  L+ SV
Sbjct: 316 RLLFGADKADSGAISIKDKPLGK-------FGSPREAIAAGIGFCSEDRKQEGAILELSV 368

Query: 367 HENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 426
            ENI L + AR  L L  + R   +    + +  LGI+    +  + +LSGGNQQK +L+
Sbjct: 369 RENIILGLQARAGL-LRVIPRKRQQAIAADYVKWLGIKTPDIETPISSLSGGNQQKALLA 427

Query: 427 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 486
           R L   P +LILDEPTRG+D+ AK EI   + AL + G+AIL ISSE+ EV+   DR+LV
Sbjct: 428 RWLATDPVILILDEPTRGIDVRAKQEIMDHVIALCRKGMAILFISSEISEVLRCSDRMLV 487

Query: 487 MREGTLAGE 495
           +R+    GE
Sbjct: 488 LRDREPCGE 496



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 66/228 (28%), Positives = 106/228 (46%), Gaps = 10/228 (4%)

Query: 29  LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARD 88
           L  ++L   AGEV+ L G  G+G++   ++L GA  AD G     D    +   P+ A  
Sbjct: 288 LAPLDLDLRAGEVYGLCGLLGSGRTETARLLFGADKADSGAISIKDKPLGKFGSPREAIA 347

Query: 89  LGVAVIYQELSLAP---NLSVAENIYLGRALQRRG----LVARGDMVRACAPTLARLGAD 141
            G+    ++         LSV ENI LG  LQ R     ++ R       A  +  LG  
Sbjct: 348 AGIGFCSEDRKQEGAILELSVRENIILG--LQARAGLLRVIPRKRQQAIAADYVKWLGIK 405

Query: 142 FSPAAN-VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEG 200
                  ++SLS   +Q   +AR +  +  IL++DEPT  +       +   +  L  +G
Sbjct: 406 TPDIETPISSLSGGNQQKALLARWLATDPVILILDEPTRGIDVRAKQEIMDHVIALCRKG 465

Query: 201 MAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248
           MAIL+IS  ++E+   +DR+ VLRD    G   R  L   ++++++ G
Sbjct: 466 MAILFISSEISEVLRCSDRMLVLRDREPCGEYLRGELDDDSVLQVIAG 513



 Score = 69.3 bits (168), Expect = 3e-16
 Identities = 60/214 (28%), Positives = 97/214 (45%), Gaps = 14/214 (6%)

Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQA 343
           S  L  GEV  L G  GAG++ L +++ G      G +R+       G    P     +A
Sbjct: 39  SLRLYPGEVHTLMGQNGAGKSTLIKVLTGVHIPEHGTIRL------NGREVRPTS-TLEA 91

Query: 344 IDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGI 403
              GI+ + ++     L  + SV ENI +    R     G ++    +R+    +  L I
Sbjct: 92  QHLGISTVYQE---VNLCPNLSVAENIFI---GRYPTKFGAIDWKTMQRQAQRLLGDLQI 145

Query: 404 RVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQS 463
            +      +       QQ V +SR L +  +VLILDEPT  +D      ++ ++  L + 
Sbjct: 146 DI-DVTAPLSRYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQLLFSVLRKLREQ 204

Query: 464 GVAILMISSELPEVVGLCDRVLVMREGTLAGEVR 497
           G+AIL ++  L +   + DR+ V+R G L GE R
Sbjct: 205 GMAILFVTHFLEQTYDISDRITVLRNGVLEGEYR 238


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: 595
Number of extensions: 31
Number of successful extensions: 8
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: 516
Length adjustment: 35
Effective length of query: 505
Effective length of database: 481
Effective search space:   242905
Effective search space used:   242905
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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

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 2024 update 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