Alignments for a candidate for HSERO_RS05250 in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Pseudovibrio axinellae Ad2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_068009665.1 PsAD2_RS19320 ATP-binding cassette domain-containing protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_001623255.1:WP_068009665.1
          Length = 497

 Score =  423 bits (1087), Expect = e-123
 Identities = 225/491 (45%), Positives = 330/491 (67%), Gaps = 5/491 (1%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           ++ L+ + K F G+  L +    + AG V AL GENGAGKSTLMKI+SG+YQRD+G +  
Sbjct: 4   LLELQGIEKSFSGINVLKSVDLTIRAGRVVALAGENGAGKSTLMKIISGIYQRDAGTVFY 63

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            G  VE T  R++   GIGIIHQELNL+  LS A+NI++GREP K +G  I  D + R++
Sbjct: 64  KGHEVEFTNARESMDAGIGIIHQELNLLPDLSVAENIYLGREPTK-LGK-IQWDVVQRES 121

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
               A+++ D+DP+TP+G+L++A+QQMVEIAKALS ++ V+IMDEPT AL + E A LF 
Sbjct: 122 KKYLAQLKQDIDPTTPLGKLSIAQQQMVEIAKALSLNAEVIIMDEPTDALTDIETAILFE 181

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
           ++ +L+AQG G+V+ISH++ E+ Q+ D ++++RDG+ +    + + S D +I  MVGR L
Sbjct: 182 VVDELRAQGKGLVFISHRLGEIFQMCDDIAILRDGQMVHQGAVADISEDDLIRHMVGREL 241

Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321
             +    P     DV +EV  L   R  +++SFT   GE++GFAGL+GAGRTE+A+AIFG
Sbjct: 242 SDQYPFVP-AEPGDVRIEVDKLT-ARGAKEISFTANAGEVVGFAGLVGAGRTELAKAIFG 299

Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF- 380
           A+P+  G + I G +  +KSP D V   IGY++EDRK  GL     + +N++L+ + RF 
Sbjct: 300 ANPIRGGSVKIDGQEISLKSPQDGVKAKIGYVTEDRKQEGLVQSQSLGSNMSLTGLDRFC 359

Query: 381 TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440
             +G +++ +       Y+   AIKT         LSGGNQQK+ IAK L+ + ++L  D
Sbjct: 360 NTLGIVNKTSEAVTISEYIEAFAIKTRDASTIISNLSGGNQQKVSIAKSLVPEPEVLILD 419

Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500
           EPTRG+DVGAK EIY L++ L  +G  I++ISS++PE+L +S R+LV+ +G++TG   R 
Sbjct: 420 EPTRGVDVGAKREIYTLINKLKAEGLCILLISSDMPELLGISDRILVLSDGKLTGSFDRD 479

Query: 501 DATQEKIMQLA 511
           +ATQE IM+ A
Sbjct: 480 EATQENIMRCA 490



 Score = 91.7 bits (226), Expect = 6e-23
 Identities = 66/226 (29%), Positives = 106/226 (46%), Gaps = 5/226 (2%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           F   AGEV    G  GAG++ L K + G      G + +DG+ + +  P+      IG +
Sbjct: 272 FTANAGEVVGFAGLVGAGRTELAKAIFGANPIRGGSVKIDGQEISLKSPQDGVKAKIGYV 331

Query: 103 HQELN---LMNHLSAAQNIFIGREPR--KAMGLFIDEDELNRQAAAIFARMRLDMDPSTP 157
            ++     L+   S   N+ +    R    +G+     E    +  I A      D ST 
Sbjct: 332 TEDRKQEGLVQSQSLGSNMSLTGLDRFCNTLGIVNKTSEAVTISEYIEAFAIKTRDASTI 391

Query: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217
           +  L+   QQ V IAK+L  +  VLI+DEPT  ++     E++ +I  L+A+G+ I+ IS
Sbjct: 392 ISNLSGGNQQKVSIAKSLVPEPEVLILDEPTRGVDVGAKREIYTLINKLKAEGLCILLIS 451

Query: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDG 263
             M EL  I+DR+ V+ DGK   +    E + + I+   V    +G
Sbjct: 452 SDMPELLGISDRILVLSDGKLTGSFDRDEATQENIMRCAVAGQTNG 497



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 59/243 (24%), Positives = 121/243 (49%), Gaps = 10/243 (4%)

Query: 277 VLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           +LE++G+ +       ++ V  T+R G ++  AG  GAG++ + + I G    +AG +  
Sbjct: 4   LLELQGIEKSFSGINVLKSVDLTIRAGRVVALAGENGAGKSTLMKIISGIYQRDAGTVFY 63

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIR 392
            G +    +  +++  GIG + ++     L   + V  NI L      T++G +    ++
Sbjct: 64  KGHEVEFTNARESMDAGIGIIHQE---LNLLPDLSVAENIYLGREP--TKLGKIQWDVVQ 118

Query: 393 EAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKS 452
             ++ Y+ QL           +L S   QQ + IAK L  + +++  DEPT  +     +
Sbjct: 119 RESKKYLAQLKQDIDPTTPLGKL-SIAQQQMVEIAKALSLNAEVIIMDEPTDALTDIETA 177

Query: 453 EIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLAT 512
            +++++D L  QGK +V IS  L E+ +M   + ++ +G++  + A AD +++ +++   
Sbjct: 178 ILFEVVDELRAQGKGLVFISHRLGEIFQMCDDIAILRDGQMVHQGAVADISEDDLIRHMV 237

Query: 513 QRE 515
            RE
Sbjct: 238 GRE 240


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: 635
Number of extensions: 34
Number of successful extensions: 8
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: 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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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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