GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Kocuria flava HO-9041

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_083529580.1 AS188_RS10235 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_001482365.1:WP_083529580.1
          Length = 492

 Score =  346 bits (887), Expect = 1e-99
 Identities = 208/479 (43%), Positives = 287/479 (59%), Gaps = 11/479 (2%)

Query: 16  LRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDG 75
           +R I K F   R L+ V+    AGEVH L GENGAGKSTLMKIL G Y+AD  GE  + G
Sbjct: 1   MRGIEKAFGVNRVLKGVDFEVLAGEVHTLAGENGAGKSTLMKILQGVYSAD-AGEIFVGG 59

Query: 76  QRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRACAPT 134
             V ID P +AR+ GV +++QE SL P LSVA+N++L R  +   GL+    MV      
Sbjct: 60  NPVTIDSPITAREAGVGMVFQEFSLVPTLSVAQNVFLNREPRNAMGLIDEDTMVEQTRAI 119

Query: 135 LARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIR 194
                    P   V  LS A  QL EIA+AV   AR+L++DEPT  LS  E++ LF LI+
Sbjct: 120 FETFEVPVDPRTPVERLSTAYWQLTEIAKAVSQNARVLILDEPTASLSKKESEILFDLIK 179

Query: 195 QLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSGF 254
           +L  +G+ I+YISHRM EI ++ DR+TV+RDG  V T     ++   LV+ ++GR L   
Sbjct: 180 RLTSQGIGIVYISHRMEEIYQVTDRITVMRDGAVVLTDHATSITPEDLVEAIIGRRLENA 239

Query: 255 YT-KTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGA 313
              +TH         L V+ ++    ++  SF +  GEVLGLAGL+G+GRTELAR +FG 
Sbjct: 240 LAYETHVVDRSGTPRLEVKRLSTDHGLEDVSFTVHPGEVLGLAGLMGSGRTELARALFGI 299

Query: 314 DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLI 373
           D    GE+ I      G  VT+    P  A++AG   + EDR+ QGL L  SV +N+ L 
Sbjct: 300 DKHRDGEILI-----DGRPVTVT--DPVSAMEAGFGLVPEDRREQGLVLSHSVRDNLLLP 352

Query: 374 VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQP 433
           + +R   G   ++   +RR   + +    ++ A   + +  LSGGNQQKV+L R +  +P
Sbjct: 353 LLSRFRKG-PLMDEGRSRRFVQDVLTKFEVKGASPGLEIRLLSGGNQQKVVLGRWVSTEP 411

Query: 434 RVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTL 492
           +VLILDEPT G+DIG K E+  LI  LA+SG A+++ISSEL E++ + DRVLV+R+G L
Sbjct: 412 KVLILDEPTAGIDIGTKGEVIELIRDLARSGTAVILISSELAELLAVSDRVLVLRKGRL 470



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 70/225 (31%), Positives = 109/225 (48%), Gaps = 7/225 (3%)

Query: 29  LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARD 88
           L  V  T + GEV  L G  G+G++ L + L G       GE  IDG+ V +  P SA +
Sbjct: 266 LEDVSFTVHPGEVLGLAGLMGSGRTELARALFGI-DKHRDGEILIDGRPVTVTDPVSAME 324

Query: 89  LGVAVIYQ---ELSLAPNLSVAENIYLGRALQ-RRG-LVARGDMVRACAPTLARLGAD-F 142
            G  ++ +   E  L  + SV +N+ L    + R+G L+  G   R     L +      
Sbjct: 325 AGFGLVPEDRREQGLVLSHSVRDNLLLPLLSRFRKGPLMDEGRSRRFVQDVLTKFEVKGA 384

Query: 143 SPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMA 202
           SP   +  LS   +Q V + R V  E ++L++DEPT  +       +  LIR L   G A
Sbjct: 385 SPGLEIRLLSGGNQQKVVLGRWVSTEPKVLILDEPTAGIDIGTKGEVIELIRDLARSGTA 444

Query: 203 ILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
           ++ IS  +AE+  ++DRV VLR G    TLDR+ +     +++ +
Sbjct: 445 VILISSELAELLAVSDRVLVLRKGRLHKTLDRSEIHDEESLQLTI 489


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: 623
Number of extensions: 42
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 540
Length of database: 492
Length adjustment: 35
Effective length of query: 505
Effective length of database: 457
Effective search space:   230785
Effective search space used:   230785
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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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