Alignments for a candidate for PS417_12065 in Phaeobacter inhibens BS107

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 GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  236 bits (603), Expect = 1e-66
 Identities = 151/481 (31%), Positives = 240/481 (49%), Gaps = 17/481 (3%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +L+ +++ K +  V A  D    L  G V AL G NGAGK+T ++IL G    D G + L
Sbjct: 15  VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
            GAP+    P  AL  G+ M+ Q       +TV ENI LG EP   G  +       R R
Sbjct: 75  FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPL-LGLGLRAGPAKARIR 133

Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185
            L +     VD  + + RL+V + Q VEI KA   D +++I+DEPT+ +   E+  LF  
Sbjct: 134 ALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFAT 193

Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245
           +R    +G  ++++SH+L E+  I+D   + R G  V   + AD D D L   +VG ++ 
Sbjct: 194 LREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADV- 252

Query: 246 RIDHKVGRECAANT----CLQVDNLSRAGE-----FHDISLQLRQGEILGIYGLMGSGRS 296
                V  + AANT     LQ+ +++            +SL L  G+I G+ G+ G+G++
Sbjct: 253 -----VPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQA 307

Query: 297 EFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIA 356
              + + GL    SGS+TL G       P+  I AG++ + EDR  +G +    +  N  
Sbjct: 308 ALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAI 367

Query: 357 LSAY-KRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLST 415
           L  Y  R S    ++ R     A+ ++    ++    +  +  +SGGN QK++L + L  
Sbjct: 368 LETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQ 427

Query: 416 EPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGR 475
            P  +L ++P RG+D GA   ++  L +    G A +++S +  E++ LSD I V   GR
Sbjct: 428 SPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGR 487

Query: 476 L 476
           L
Sbjct: 488 L 488



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 63/248 (25%), Positives = 117/248 (47%), Gaps = 10/248 (4%)

Query: 250 KVGRECAANTCLQVDNLS-RAGEF---HDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305
           K+G+       L++ N++ R G      D+S  L  GE++ + G  G+G++  +N ++G 
Sbjct: 5   KMGQAPGLTPVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQ 64

Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365
            +AD+G V L G P+P G P+A ++ G+ +V    +   L    ++  NI L     L  
Sbjct: 65  YMADTGGVELFGAPLPPGAPRAALDGGVGMV---HQHFTLADNLTVWENITLGVEPLLGL 121

Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425
                  K    A  + ++  +K       V+ ++ G +Q+V + K L  +   L+ DEP
Sbjct: 122 GLRAGPAKARIRA--LAEQFHLKVDP-NAKVSRLTVGERQRVEILKALYRDARILILDEP 178

Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485
           T  +       ++  L + +  G + I +S +  E++ +SDR+ V + G+LV        
Sbjct: 179 TAVLTPQESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADT 238

Query: 486 SQEALLRL 493
             +AL  L
Sbjct: 239 DSDALAAL 246


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: 543
Number of extensions: 24
Number of successful extensions: 7
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: 522
Length adjustment: 34
Effective length of query: 461
Effective length of database: 488
Effective search space:   224968
Effective search space used:   224968
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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Rules (tab-delimited)
Protein sequences (fasta format)
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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