GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2274
          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:

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:

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:

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:

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