Alignments for a candidate for HSERO_RS05250 in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Streptacidiphilus oryzae TH49

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_051939879.1 BS73_RS13055 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_000744815.1:WP_051939879.1
          Length = 540

 Score =  388 bits (997), Expect = e-112
 Identities = 210/511 (41%), Positives = 320/511 (62%), Gaps = 10/511 (1%)

Query: 6   ETSTTGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLM 65
           E +T      + +  PV+ +  V K F GV AL    F L  GEVHAL+GENGAGKSTL+
Sbjct: 4   EPTTAAGPTGTGTPRPVLEVAGVSKAFAGVQALSEVDFTLLPGEVHALIGENGAGKSTLI 63

Query: 66  KILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPR 125
           K+++GV+Q DSG + L G+      P +AQA G+  I+QE+NL+  +S A+N+++GREPR
Sbjct: 64  KVVTGVHQPDSGTVRLAGEERRFGNPLEAQAAGLSTIYQEVNLVPLMSVARNLYLGREPR 123

Query: 126 KAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMD 185
           + +GL ID   +NR AA   AR  +++D + P+  L +  QQMV +A+A+  D+RV+IMD
Sbjct: 124 R-LGL-IDTRRMNRDAAEALARYGVEVDVTRPLRTLGLGAQQMVALARAVQIDARVVIMD 181

Query: 186 EPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQ 245
           EPT++L   E+  LF +IR+L+ Q + +VY+SH++DEL  + DRV+VMRDG+ + T  M 
Sbjct: 182 EPTSSLEPREVETLFSVIRELKRQSIAVVYVSHRLDELYAVCDRVTVMRDGRVVHTGEMA 241

Query: 246 ETSMDTIISMMVGRALD---GEQRIPPDTSRNDV-----VLEVRGLNRGRAIRDVSFTLR 297
                 +IS+M+GR +     E     D+ R+        L   GL     +  VSF + 
Sbjct: 242 GLERLRLISLMLGREMSTVRSEGSTAFDSDRHHAKDGVPALRAEGLTVRHRLDGVSFEIH 301

Query: 298 KGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDR 357
            GE++G  GL+GAGR+E A+A+ GA P E+GE+ + G     +SPA A+  G+  L EDR
Sbjct: 302 PGEVVGLGGLLGAGRSETAKAVVGALPAESGEVEVGGKPLRRRSPAAAIRAGVVMLPEDR 361

Query: 358 KHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLS 417
           K  G+   + V+ NI+L+++ R +R G + +    E    ++++L IK  S +Q  R LS
Sbjct: 362 KVEGIIPSLSVRENISLAALPRLSRAGLVSRAKQDEVVDFFMKRLRIKASSPDQPVRDLS 421

Query: 418 GGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPE 477
           GGNQQK+++A+WL     +L  DEPTRGIDVGAK+E+  L+D LA  G  +++ISS+L E
Sbjct: 422 GGNQQKVMLARWLCLSPKVLLLDEPTRGIDVGAKAEVQGLIDELAADGLGVLLISSDLEE 481

Query: 478 VLRMSHRVLVMCEGRITGELARADATQEKIM 508
           ++  + RV+V+ +GR+ G L     ++E ++
Sbjct: 482 LIEGADRVVVLKDGRVVGGLDGDQVSEEGLL 512



 Score =  105 bits (263), Expect = 3e-27
 Identities = 65/223 (29%), Positives = 117/223 (52%), Gaps = 4/223 (1%)

Query: 38  LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQAL 97
           LD   FE+  GEV  L G  GAG+S   K + G    +SG++ + GKP+    P  A   
Sbjct: 293 LDGVSFEIHPGEVVGLGGLLGAGRSETAKAVVGALPAESGEVEVGGKPLRRRSPAAAIRA 352

Query: 98  GIGIIHQELN---LMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMD- 153
           G+ ++ ++     ++  LS  +NI +   PR +    +   + +        R+R+    
Sbjct: 353 GVVMLPEDRKVEGIIPSLSVRENISLAALPRLSRAGLVSRAKQDEVVDFFMKRLRIKASS 412

Query: 154 PSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGI 213
           P  PV +L+   QQ V +A+ L    +VL++DEPT  ++    AE+  +I +L A G+G+
Sbjct: 413 PDQPVRDLSGGNQQKVMLARWLCLSPKVLLLDEPTRGIDVGAKAEVQGLIDELAADGLGV 472

Query: 214 VYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMM 256
           + IS  ++EL + ADRV V++DG+ +  +   + S + +++ +
Sbjct: 473 LLISSDLEELIEGADRVVVLKDGRVVGGLDGDQVSEEGLLAAL 515


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: 703
Number of extensions: 31
Number of successful extensions: 7
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: 520
Length of database: 540
Length adjustment: 35
Effective length of query: 485
Effective length of database: 505
Effective search space:   244925
Effective search space used:   244925
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