Alignments for a candidate for HSERO_RS05250 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  431 bits (1109), Expect = e-125
 Identities = 231/488 (47%), Positives = 318/488 (65%), Gaps = 2/488 (0%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           PV+ L  + K FPGV ALD     +  GEVHALMGENGAGKSTLMK+L G++Q D G I+
Sbjct: 6   PVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQII 65

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140
           +  +PV ++ P  A+A GI  IHQEL+L + LS A+NI++G  PRK  GL +D  EL  +
Sbjct: 66  VAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGL-VDWAELEAK 124

Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200
             AI  ++++  +  T VG+L++A QQMVEIA+AL+ D++ +I DEPTA+L +AE   LF
Sbjct: 125 TNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLF 184

Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
            +I DLQ QGVGI YISH+M+E+ +I DR+SV+RDG+Y  TV   ET+ + +  MM+GR 
Sbjct: 185 EVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRK 244

Query: 261 LDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320
           LD   R        +V LEVRGL+ G    DV+F +R+GE++GF GL+GAGRTE+A  +F
Sbjct: 245 LD-LSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLF 303

Query: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380
           G     +G I + G +  I SP DA+  GI  + EDRK  GL +GM+ + N+ L  +   
Sbjct: 304 GLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDL 363

Query: 381 TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440
               F+   A       Y  +L I+TP  +Q    LSGGNQQKIVI KWL    ++L  D
Sbjct: 364 KAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVD 423

Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500
           EPTRGIDVG+K+EI+ LL  LA QG A+++ISSE+PEVL ++ R++ M  GRI       
Sbjct: 424 EPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSE 483

Query: 501 DATQEKIM 508
           + T+E ++
Sbjct: 484 EVTEENLI 491



 Score =  110 bits (275), Expect = 1e-28
 Identities = 75/235 (31%), Positives = 120/235 (51%), Gaps = 14/235 (5%)

Query: 39  DNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALG 98
           ++  FE+  GEV    G  GAG++ + + L G+    SG I LDG  V IT P  A   G
Sbjct: 273 EDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERG 332

Query: 99  IGIIHQELN---LMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPS 155
           I ++ ++     L+  ++   N+ + +      G F+ +        AIF + R  +D  
Sbjct: 333 ISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGA----EIAIFDQYRDKLDIR 388

Query: 156 TP-----VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQG 210
           TP     VG L+   QQ + I K LS    VLI+DEPT  ++    AE+  ++RDL AQG
Sbjct: 389 TPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQG 448

Query: 211 VGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQ 265
             ++ IS +M E+  +ADR+  M  G+ + T   +E + + +I+ + G  LD E+
Sbjct: 449 YAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG--LDTEK 501



 Score = 98.2 bits (243), Expect = 6e-25
 Identities = 64/229 (27%), Positives = 114/229 (49%), Gaps = 5/229 (2%)

Query: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAV 346
           RA+  VS T+  GE+    G  GAG++ + + + G    + G+II+     V+  P DA 
Sbjct: 21  RALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIVAEQPVVMSGPLDAK 80

Query: 347 AHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKT 406
           A GI ++ ++     LA  + V  NI L  + R  R G +D   +       + +L +  
Sbjct: 81  AKGIVFIHQE---LSLADELSVAENIYLGELPR-KRFGLVDWAELEAKTNAILEKLKVGF 136

Query: 407 PSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466
            + + +   LS  NQQ + IA+ L  D   + FDEPT  +    K  +++++  L EQG 
Sbjct: 137 -NAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEVISDLQEQGV 195

Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515
            I  IS  + E+ +++ R+ V+ +G+  G +  A+  +E + Q+   R+
Sbjct: 196 GIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRK 244


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: 619
Number of extensions: 32
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: 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 Sep 17 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 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