Aligments for a candidate for PS417_12065 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for PS417_12065 in Phaeobacter inhibens BS107

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= uniprot:A0A1N7TX47
         (495 letters)



>lcl|FitnessBrowser__Phaeo:GFF2274 PGA1_c23060 ribose import
           ATP-binding protein RbsA
          Length = 503

 Score =  331 bits (849), Expect = 3e-95
 Identities = 188/490 (38%), Positives = 285/490 (58%), Gaps = 1/490 (0%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +L+ E + K + GV AL    L++  G VHAL G NGAGKST + +L GI Q D G I++
Sbjct: 7   VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIV 66

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
              PV  + P +A A GI  I QEL     ++VAENI+LG  PR+   +VD   L  +T 
Sbjct: 67  AEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKTN 126

Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185
            +L+ L+   +A + +  LS+A  Q+VEIA+A + D + +I DEPT+++ + E   LF+ 
Sbjct: 127 AILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186

Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245
           I  L  QG GI Y+SHR+ E+ +I D  S+ RDG +  +   A+ + +++ + ++G++L 
Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246

Query: 246 RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305
              ++   E      L+V  LS    F D++ ++R+GE++G YGL+G+GR+E    ++GL
Sbjct: 247 LSRNEAHHELG-EVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGL 305

Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365
               SGS+ L G  + I  P   I  G+SLV EDRK  GLVL  +   N+ L     L +
Sbjct: 306 RNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKA 365

Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425
              +    E  + +    +L I+T   +  V ++SGGNQQK+V+ K LS  P  L+ DEP
Sbjct: 366 GPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEP 425

Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485
           TRGID G+K EI++LL      G A IV+SSE PE+LH++DRI     GR++   T   +
Sbjct: 426 TRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEV 485

Query: 486 SQEALLRLAS 495
           ++E L+   S
Sbjct: 486 TEENLIAAIS 495



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 56/229 (24%), Positives = 101/229 (44%), Gaps = 5/229 (2%)

Query: 24  DGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGI 83
           D    +R G V    G  GAG++     L G+    +GSI L+GA V    P +A+  GI
Sbjct: 274 DVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGI 333

Query: 84  AMITQELEP---IPYMTVAENIWLGR-EPRRAGCIVDNKALNRRTRELLDSLEFDVDATS 139
           +++ ++ +    +  M   +N+ L + +  +AG  V + A      +  D L+       
Sbjct: 334 SLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWK 393

Query: 140 PM-HRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIVY 198
            +   LS    Q + I K  S    V+I+DEPT  I       +   +R L AQG  ++ 
Sbjct: 394 QLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIV 453

Query: 199 VSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTRI 247
           +S  + E+  +AD       G  + +    ++  ++L+  I G +  ++
Sbjct: 454 ISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTEKV 502


Lambda     K      H
   0.319    0.135    0.381 

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: 538
Number of extensions: 26
Number of successful extensions: 6
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: 495
Length of database: 503
Length adjustment: 34
Effective length of query: 461
Effective length of database: 469
Effective search space:   216209
Effective search space used:   216209
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, or view the source code.

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