Alignments for a candidate for araG in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Phaeobacter inhibens BS107

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  375 bits (964), Expect = e-108
 Identities = 210/494 (42%), Positives = 305/494 (61%), Gaps = 3/494 (0%)

Query: 1   MQQSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPT 60
           M + +P L   GI KTFPGV+AL  +S     G+VHALMGENGAGKSTL+K+L G + P 
Sbjct: 1   MTEQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD 60

Query: 61  TGSVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKG-GIVNRSL 119
            G +++  Q +  S    A   G+  I+QEL L  E++VAENIYLG+LP K  G+V+ + 
Sbjct: 61  EGQIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAE 120

Query: 120 LNYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREI 179
           L  +    L+ L +  +  T +  LSI   QMVEIA+AL  +AK + FDEPT+SL+  E 
Sbjct: 121 LEAKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEK 180

Query: 180 DNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239
             LF VI +L+++G  I Y+SHRMEEIF ++D I+V +DG+Y  T  +  + + + + Q 
Sbjct: 181 VVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGT-VNTAETNEENVTQM 239

Query: 240 MVGRDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELM 299
           M+GR +           GE  L +  +    +   ++  VR GE+VG +GLVGAGR+E+ 
Sbjct: 240 MIGRKLDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIA 299

Query: 300 KGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISA 359
           + +FG    T+G +++D   + I  P  AI  G+ L PEDRK +G++   + RDN+ +  
Sbjct: 300 ETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLP- 358

Query: 360 RRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMK 419
           +   +  G  + +G E    D +   L+I+TPG +QL+ NLSGGNQQK ++G+WLS    
Sbjct: 359 QVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPN 418

Query: 420 VILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAG 479
           V+++DEPTRGIDVG+K EI+N++  LAAQG AV+  SS++PEVL VADRIV M  G I  
Sbjct: 419 VLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMR 478

Query: 480 ELLHEQADERQALS 493
               E+  E   ++
Sbjct: 479 TFTSEEVTEENLIA 492



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 73/248 (29%), Positives = 116/248 (46%), Gaps = 30/248 (12%)

Query: 261 LRLDAVKA--PGVRT--PISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYID 316
           LRL+ +    PGVR    +SL +  GE+  L G  GAG+S LMK + G  Q   GQ+ + 
Sbjct: 8   LRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIVA 67

Query: 317 QQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVH---------SVRDNINISARRKHVLGG 367
           +QP+            +M  P D KA+GI+ +H         SV +NI +    +   G 
Sbjct: 68  EQPV------------VMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGL 115

Query: 368 CVINNGWEENNADHHIRSLNIKTP-GAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEP 426
                 W E  A  +     +K    A+  + +LS  NQQ   + R L+ + K ++ DEP
Sbjct: 116 V----DWAELEAKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEP 171

Query: 427 TRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQA 486
           T  +    K  ++ VI  L  QGV + + S  + E+  + DRI V+R+G+  G +   + 
Sbjct: 172 TASLTDAEKVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAET 231

Query: 487 DERQALSL 494
           +E     +
Sbjct: 232 NEENVTQM 239


Lambda     K      H
   0.319    0.136    0.391 

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: 654
Number of extensions: 34
Number of successful extensions: 8
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: 504
Length of database: 503
Length adjustment: 34
Effective length of query: 470
Effective length of database: 469
Effective search space:   220430
Effective search space used:   220430
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