Alignments for a candidate for H281DRAFT_01113 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Phaeobacter inhibens BS107

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  333 bits (854), Expect = 9e-96
 Identities = 191/497 (38%), Positives = 292/497 (58%), Gaps = 8/497 (1%)

Query: 14  PFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLV 73
           P L + G+ K F GV AL GVSL+   G+++ L+GENG GKSTL+K++ G   PDEGQ++
Sbjct: 6   PVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQII 65

Query: 74  IEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVL 133
           +   P      L+A A GI  ++Q+LSL   +SVAEN+ L  EL      L    D   L
Sbjct: 66  VAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYL-GELPRKRFGLV---DWAEL 121

Query: 134 AATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQK 193
            A     LE + +  N++   T +  L +A +Q+V IARA+  +AK VI DEPT SLT  
Sbjct: 122 EAKTNAILEKLKVGFNAK---TRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDA 178

Query: 194 EVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISE 253
           E   L  V+++L+ QGV + ++SH+++E + I   + VLRDGQ       AE  +  +++
Sbjct: 179 EKVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQ 238

Query: 254 LMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNEL 313
           +M GR L   R        ++ L+VRG +    F DV+F++  GE++G  GL+ +GR E+
Sbjct: 239 MMIGRKLDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEI 298

Query: 314 ARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITA 373
           A  L G+    SG + LDG ++A+ +P DA    I  VPEDR  +GL L    RDN+   
Sbjct: 299 AETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLP 358

Query: 374 MISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDP 433
            +  L+      D     A+ +Q   +L I TPG  + V +LSGGNQQ+++IG+WL++ P
Sbjct: 359 QVDDLKAGPFVADGAEI-AIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRP 417

Query: 434 RVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVS 493
            VLI+  PT G+DVGSK  I+ +++ L+ +G  +I+IS ++PE+L   DRI+ M  G + 
Sbjct: 418 NVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIM 477

Query: 494 AEYRADELSEADLYHAL 510
             + ++E++E +L  A+
Sbjct: 478 RTFTSEEVTEENLIAAI 494



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 55/234 (23%), Positives = 109/234 (46%), Gaps = 6/234 (2%)

Query: 278 VRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIAL 337
           V+ F        VS  +  GE+  + G   +G++ L + L G+     G +++  Q + +
Sbjct: 14  VKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIVAEQPVVM 73

Query: 338 RTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQT 397
             P DAK   I ++ ++     L  +  + +N+    +   R RFG +D    +A     
Sbjct: 74  SGPLDAKAKGIVFIHQEL---SLADELSVAENIYLGELP--RKRFGLVDWAELEAKTNAI 128

Query: 398 VKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIM 457
           +++L++      + V  LS  NQQ V I R L +D + +I   PT  +    K +++ ++
Sbjct: 129 LEKLKVGFNAKTR-VGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEVI 187

Query: 458 QRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511
             L ++G+GI  IS  + E+ +  DRI +++ G         E +E ++   ++
Sbjct: 188 SDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMI 241



 Score = 57.4 bits (137), Expect = 1e-12
 Identities = 50/230 (21%), Positives = 100/230 (43%), Gaps = 14/230 (6%)

Query: 34  VSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGIE 93
           V+   +RG++    G  G G++ + + + G + P  G + ++G   A  S  +A+  GI 
Sbjct: 275 VNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGIS 334

Query: 94  TVYQDLS---LLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLPGNS 150
            V +D     L+  M+  +N+ L        G          +       L+ +  PG  
Sbjct: 335 LVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLD-IRTPGWK 393

Query: 151 EFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSL---TQKEVDNLIAVLANLRA 207
           +    L+  L    +Q + I + ++     +I+DEPT  +   ++ E+ NL   L +L A
Sbjct: 394 Q----LVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNL---LRDLAA 446

Query: 208 QGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
           QG  V+ +S ++ E   +   ++ +  G+ M      E T+  +   ++G
Sbjct: 447 QGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496


Lambda     K      H
   0.319    0.135    0.376 

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: 580
Number of extensions: 35
Number of successful extensions: 6
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: 515
Length of database: 503
Length adjustment: 34
Effective length of query: 481
Effective length of database: 469
Effective search space:   225589
Effective search space used:   225589
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 (21.7 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