Alignments for a candidate for frcA in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Tistlia consotensis USBA 355

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_085126169.1 B9O00_RS28465 multiple monosaccharide ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_900177295.1:WP_085126169.1
          Length = 509

 Score =  353 bits (905), Expect = e-101
 Identities = 229/514 (44%), Positives = 306/514 (59%), Gaps = 29/514 (5%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71
           +L +R+I KTFPGV AL  V L    GE+HAL GENGAGKSTLMKILSG Y   D  G+ 
Sbjct: 4   ILEMRDITKTFPGVVALDNVNLQVRQGEIHALAGENGAGKSTLMKILSGVYPYGDYQGDI 63

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
             +G+  +  G   +   G+ +I+QEL+L P LS+AENI+LG  + R G++         
Sbjct: 64  VYEGEVKKFRGIADSEAEGIVIIHQELALVPELSIAENIFLGNEIARFGVIDWHATNELA 123

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
           A  L  +G   SP   V  L + ++QLVEIA+A+  E ++L++DEPT+ L+  ++  L  
Sbjct: 124 ADHLKWVGLKESPRTKVQDLGLGKQQLVEIAKALSKEVKLLILDEPTSSLNEQDSAALLK 183

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD--RAHLSQAALVKMMVGR 249
           L+ + R  G++ + ISH++ EI ++AD +TVLRDG  V TLD   A +S+  +++ MVGR
Sbjct: 184 LLAEFRERGISSILISHKLNEISQVADSITVLRDGTTVSTLDCAAASISEDDIIRDMVGR 243

Query: 250 DLSGFYTKTH---GQAVEREVMLSVR--DVADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304
            LS  +   H   G+ +      SVR     D R VK  SF +R GEV+GLAGL+GAGRT
Sbjct: 244 SLSDRFPPRHPKIGELLLEVEHWSVRHPQHLDRRVVKDASFTVRRGEVVGLAGLMGAGRT 303

Query: 305 ELARLVFGAD--ARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362
           ELA  +FG    A   GEVRI   A     V        +AI AG+ Y TEDRK  GL L
Sbjct: 304 ELAMSLFGRSYGADIAGEVRIRGKAVDVSTV-------ERAIAAGLCYATEDRKSYGLVL 356

Query: 363 DQSVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGG 418
           D  V  N+ L     VA    +   R  R A   R    I T  I  A   +N   LSGG
Sbjct: 357 DDIVKHNLTLANLEGVANGPVIDHAREIRVAEDYRRRLNIKTSSI--AQKTLN---LSGG 411

Query: 419 NQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVV 478
           NQQKV+L + L   P VLILDEPTRG+D+GAK EIY +I  LA +G  IL+ISSE+PE++
Sbjct: 412 NQQKVVLGKWLFADPEVLILDEPTRGIDVGAKYEIYSIITDLAAAGKGILVISSEMPELL 471

Query: 479 GLCDRVLVMREGTLAGEVRPAGSAAETQERIIAL 512
           G+CDR+ VM  G L GE+ PA  A  +QE+I+++
Sbjct: 472 GICDRIYVMNAGRLVGEL-PAAEA--SQEKIMSM 502



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 61/231 (26%), Positives = 104/231 (45%), Gaps = 13/231 (5%)

Query: 27  RALRKVELTAYAGEVHALMGENGAGKSTL-MKILSGAYTADPGGECHIDGQRVQIDGPQS 85
           R ++    T   GEV  L G  GAG++ L M +   +Y AD  GE  I G+ V +   + 
Sbjct: 277 RVVKDASFTVRRGEVVGLAGLMGAGRTELAMSLFGRSYGADIAGEVRIRGKAVDVSTVER 336

Query: 86  ARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADFSPA 145
           A   G+    ++   +  L + + +     L     VA G ++        R+  D+   
Sbjct: 337 AIAAGLCYATEDRK-SYGLVLDDIVKHNLTLANLEGVANGPVIDHAREI--RVAEDYRRR 393

Query: 146 ANVASLSIAQRQL---------VEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
            N+ + SIAQ+ L         V + + +  +  +L++DEPT  +       ++++I  L
Sbjct: 394 LNIKTSSIAQKTLNLSGGNQQKVVLGKWLFADPEVLILDEPTRGIDVGAKYEIYSIITDL 453

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
              G  IL IS  M E+  + DR+ V+  G  VG L  A  SQ  ++ M++
Sbjct: 454 AAAGKGILVISSEMPELLGICDRIYVMNAGRLVGELPAAEASQEKIMSMII 504


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: 627
Number of extensions: 29
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: 2
Length of query: 540
Length of database: 509
Length adjustment: 35
Effective length of query: 505
Effective length of database: 474
Effective search space:   239370
Effective search space used:   239370
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 Apr 09 2024. 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:

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