Alignments for a candidate for HSERO_RS05250 in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078427229.1 BK574_RS01730 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_002019605.1:WP_078427229.1
          Length = 503

 Score =  325 bits (834), Expect = 2e-93
 Identities = 178/484 (36%), Positives = 291/484 (60%), Gaps = 3/484 (0%)

Query: 30  KRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEIT 89
           K F G  AL +   ++ AGEVH+L+GENGAGKSTL+KI++GVYQ  +G I  + + V++ 
Sbjct: 11  KHFGGNHALKDITLKIKAGEVHSLVGENGAGKSTLIKIVTGVYQPTNGTIKWENEKVKVQ 70

Query: 90  EPRQAQALGIGIIHQELNLMNHLSAAQNIFIGRE-PRKAMGLFIDEDELNRQAAAIFARM 148
            P+ AQ LGI +IHQ+  L+ + +  +N+F+ ++ P+K  G+ ID + + +QA A+    
Sbjct: 71  TPKAAQQLGINVIHQDRQLVPYFTGLENLFLNQDYPKKKFGIGIDWNAMKQQADALQEEW 130

Query: 149 RLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQA 208
            + +  ST V  ++ + + ++EI +A+  +S++LI+DEPTAAL + E   LF  IR L+ 
Sbjct: 131 GIQLPLSTLVSNMSPSERTLLEILRAMMMESKLLILDEPTAALTDKESELLFSFIRRLKE 190

Query: 209 QGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG-RALDGEQRI 267
           +GV IVY+SH+++E+ Q++D+V+V+  GK   T+  +E S +TII  M G +A+   +  
Sbjct: 191 KGVAIVYVSHRLEEVIQLSDQVTVLIGGKIATTLTKKELSKETIIEYMTGGKAIKALKER 250

Query: 268 PPDTSRNDVVLEVRGLN-RGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLE 326
             +     ++L V+GL  + + ++ V   L KGEILG  GL GAGRTE+  AI+G   +E
Sbjct: 251 SDEKRSEQILLSVKGLKTKDQVVKSVDLQLHKGEILGIYGLAGAGRTELLEAIYGLRKIE 310

Query: 327 AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFM 386
           AG I          SP  ++ +G+  + E+R    L +G  ++ N+ L  +   T+ G +
Sbjct: 311 AGSIQFENNVIEKISPNKSIENGVVLIPENRHDDALIMGNTIRENMTLPILSDLTKRGVI 370

Query: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGI 446
            ++   +  +  + +  +K    EQ    LSGGNQQK+V AK LL    I   DEPT+ +
Sbjct: 371 QRKQEFQFVEQEMERFKVKATGSEQTVSELSGGNQQKVVFAKALLCQPTIYLCDEPTQAV 430

Query: 447 DVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEK 506
           DV  ++EI++ L   A++GK I+ +SS+LPEVL +S R++VM EG    EL        +
Sbjct: 431 DVMTRAEIHRFLQNQADEGKGIIFVSSDLPEVLEISDRIVVMNEGETVAELVNHHLQPNE 490

Query: 507 IMQL 510
           ++ +
Sbjct: 491 VLDI 494



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 57/241 (23%), Positives = 116/241 (48%), Gaps = 9/241 (3%)

Query: 277 VLEVRGLNR----GRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           +LE+  LN+      A++D++  ++ GE+    G  GAG++ + + + G      G I  
Sbjct: 3   LLEIDQLNKHFGGNHALKDITLKIKAGEVHSLVGENGAGKSTLIKIVTGVYQPTNGTIKW 62

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGF-MDQRAI 391
              K  +++P  A   GI  + +DR+      G++   N+ L+      + G  +D  A+
Sbjct: 63  ENEKVKVQTPKAAQQLGINVIHQDRQLVPYFTGLE---NLFLNQDYPKKKFGIGIDWNAM 119

Query: 392 REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAK 451
           ++ A     +  I+ P +      +S   +  + I + ++ +  +L  DEPT  +     
Sbjct: 120 KQQADALQEEWGIQLP-LSTLVSNMSPSERTLLEILRAMMMESKLLILDEPTAALTDKES 178

Query: 452 SEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLA 511
             ++  +  L E+G AIV +S  L EV+++S +V V+  G+I   L + + ++E I++  
Sbjct: 179 ELLFSFIRRLKEKGVAIVYVSHRLEEVIQLSDQVTVLIGGKIATTLTKKELSKETIIEYM 238

Query: 512 T 512
           T
Sbjct: 239 T 239


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: 537
Number of extensions: 21
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: 503
Length adjustment: 35
Effective length of query: 485
Effective length of database: 468
Effective search space:   226980
Effective search space used:   226980
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