GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Klebsiella michiganensis M5al

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BWI76_RS18245 BWI76_RS18245 L-arabinose transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Koxy:BWI76_RS18245
          Length = 504

 Score =  370 bits (949), Expect = e-107
 Identities = 220/489 (44%), Positives = 301/489 (61%), Gaps = 17/489 (3%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P L+   I  TFPGV+AL  +    YAG+VHALMGENGAGKSTL+KILSG Y     G  
Sbjct: 6   PYLSFHGITMTFPGVKALSDISFGCYAGQVHALMGENGAGKSTLLKILSGNYIPT-AGSL 64

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
            I GQ++  +    A + GVA+IYQEL L P ++VAENIYLG+   + G+V R  +    
Sbjct: 65  QIRGQQMTFNHTTEALNAGVAIIYQELHLIPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              L  LG D  P   +  LSI Q Q+VEIA+A+   A+I+  DEPT+ LS  E + LF 
Sbjct: 125 GLQLKHLGLDIDPETPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIENLFR 184

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAH-LSQAALVKMMVGRD 250
           +IR+LR EG  I+Y+SHRM EI  L+D +TV +DG +V T D    ++  ALV+ MVGR+
Sbjct: 185 VIRELRQEGRVIIYVSHRMEEIFALSDAITVFKDGRYVRTFDNMQEVNHDALVQAMVGRE 244

Query: 251 LSGFY---TKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307
           L   Y    + +G+  ER  +  V+  A G R +  S  +R+GE++GL GLVGAGR+EL 
Sbjct: 245 LGNIYGWQPREYGK--ERLRLEQVK--APGVR-QPVSLSVRSGEIVGLFGLVGAGRSELM 299

Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367
           + +FG    T G+V I   A       +    P QAI AG+    EDRK +G+    SV 
Sbjct: 300 KGLFGGSRITGGQVYIDGEA-------IDIRKPAQAIQAGMMLCPEDRKAEGIIPVHSVR 352

Query: 368 ENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 427
           +NIN+    +  L    +N     +   + I +L I+   A+  +  LSGGNQQK +L R
Sbjct: 353 DNINISARRKHILAGCVINNAWEAQNADQHIKSLNIKTPGAEQLIMNLSGGNQQKAILGR 412

Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487
            L  + +V++LDEPTRG+D+GAK EIY +I ALA SGVA++  SS+LPEV+G+ DR++VM
Sbjct: 413 WLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAASGVAVVFASSDLPEVLGVADRIVVM 472

Query: 488 REGTLAGEV 496
           REG +AGE+
Sbjct: 473 REGEIAGEL 481



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 62/223 (27%), Positives = 108/223 (48%), Gaps = 10/223 (4%)

Query: 24  PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83
           PGVR  + V L+  +GE+  L G  GAG+S LMK L G  +   GG+ +IDG+ + I  P
Sbjct: 269 PGVR--QPVSLSVRSGEIVGLFGLVGAGRSELMKGLFGG-SRITGGQVYIDGEAIDIRKP 325

Query: 84  QSARDLGVAVIYQELS---LAPNLSVAENIYLGRALQR--RGLVARGDMVRACAPTLARL 138
             A   G+ +  ++     + P  SV +NI +    +    G V         A    + 
Sbjct: 326 AQAIQAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHILAGCVINNAWEAQNADQHIKS 385

Query: 139 GADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
               +P A   + +LS   +Q   + R +  E +++++DEPT  +       ++ +I  L
Sbjct: 386 LNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYAL 445

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239
              G+A+++ S  + E+  +ADR+ V+R+G   G L   H ++
Sbjct: 446 AASGVAVVFASSDLPEVLGVADRIVVMREGEIAGELLHEHANE 488


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: 625
Number of extensions: 29
Number of successful extensions: 9
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: 504
Length adjustment: 35
Effective length of query: 505
Effective length of database: 469
Effective search space:   236845
Effective search space used:   236845
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