Alignments for a candidate for HSERO_RS05250 in Photobacterium gaetbulicola Gung47

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Photobacterium gaetbulicola Gung47

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_039469450.1 H744_RS03175 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_000940995.1:WP_039469450.1
          Length = 497

 Score =  461 bits (1187), Expect = e-134
 Identities = 244/492 (49%), Positives = 339/492 (68%), Gaps = 3/492 (0%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           ++ +R + K FPGV ALDN Q  L  G V ALMGENGAGKSTLMK+L G YQRD G I  
Sbjct: 5   ILEMRGITKTFPGVKALDNVQLTLKKGRVMALMGENGAGKSTLMKVLFGTYQRDEGTIRY 64

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            G+ V+ +  +++   GI +IHQEL+ + H + A+NI++GREP       ID  ++    
Sbjct: 65  QGELVDFSGAKESLESGISMIHQELSPVLHRNIAENIWLGREPLTGPLRLIDHKKMFADT 124

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
            A+  R+ LD+DP T + +LTVA  QMVEIAKA+SF+S+++IMDEPT+AL + E+A LF 
Sbjct: 125 EALLQRLDLDLDPRTLMSDLTVATMQMVEIAKAISFESKIIIMDEPTSALTDKEVAHLFE 184

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
           II  L++QGV +VYISHKMDE+ +I D ++V RDG YI     ++T+ D ++ MMVGR L
Sbjct: 185 IIEKLKSQGVAMVYISHKMDEIFKICDDITVFRDGCYIGEREARDTNHDELVQMMVGRDL 244

Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321
            G+   PP      + LEV+ L+     + V+F L +GEILG AGL+GAGRTE+   +FG
Sbjct: 245 -GDVFPPPTAKPGKIRLEVKNLSVDGCFKHVNFKLHEGEILGIAGLVGAGRTELIETLFG 303

Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF- 380
               E GEI I+G +  IK+P DA++H + +L+EDR+H GL + +D+ AN +++ +  + 
Sbjct: 304 VREKETGEIWINGEEVEIKAPQDAISHKMAFLTEDRRHSGLYLMLDIFANTSIAHLDAYK 363

Query: 381 TRV-GFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFF 439
           +RV   +D R +R  ++ + ++L +KTP + +    LSGGNQQK+++A+W+L   DILF 
Sbjct: 364 SRVANVLDVRQMRSDSEEHCKKLKVKTPHMSEAIDNLSGGNQQKVLLARWMLTKPDILFL 423

Query: 440 DEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELAR 499
           DEPTRGIDVGAKSEIYKL+  L   GK++VMISSELPEV+ MS RVLVM EG + GEL  
Sbjct: 424 DEPTRGIDVGAKSEIYKLMRLLTGMGKSLVMISSELPEVIGMSDRVLVMHEGNLKGELDG 483

Query: 500 ADATQEKIMQLA 511
            +ATQEKIM +A
Sbjct: 484 TEATQEKIMSMA 495



 Score = 76.3 bits (186), Expect = 2e-18
 Identities = 52/246 (21%), Positives = 115/246 (46%), Gaps = 8/246 (3%)

Query: 274 NDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGE 329
           + V+LE+RG+ +     +A+ +V  TL+KG ++   G  GAG++ + + +FG    + G 
Sbjct: 2   SQVILEMRGITKTFPGVKALDNVQLTLKKGRVMALMGENGAGKSTLMKVLFGTYQRDEGT 61

Query: 330 IIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQR 389
           I   G         +++  GI  + ++       +  ++  NI L        +  +D +
Sbjct: 62  IRYQGELVDFSGAKESLESGISMIHQE---LSPVLHRNIAENIWLGREPLTGPLRLIDHK 118

Query: 390 AIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVG 449
            +    +  +++L +        + L +    Q + IAK +  +  I+  DEPT  +   
Sbjct: 119 KMFADTEALLQRLDLDLDPRTLMSDL-TVATMQMVEIAKAISFESKIIIMDEPTSALTDK 177

Query: 450 AKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQ 509
             + ++++++ L  QG A+V IS ++ E+ ++   + V  +G   GE    D   ++++Q
Sbjct: 178 EVAHLFEIIEKLKSQGVAMVYISHKMDEIFKICDDITVFRDGCYIGEREARDTNHDELVQ 237

Query: 510 LATQRE 515
           +   R+
Sbjct: 238 MMVGRD 243


Lambda     K      H
   0.320    0.135    0.372 

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: 651
Number of extensions: 33
Number of successful extensions: 7
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: 520
Length of database: 497
Length adjustment: 34
Effective length of query: 486
Effective length of database: 463
Effective search space:   225018
Effective search space used:   225018
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:

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