Alignments for a candidate for araVsh in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Phaeobacter inhibens BS107

Align ABC transporter related (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  356 bits (913), Expect = e-102
 Identities = 190/497 (38%), Positives = 314/497 (63%), Gaps = 7/497 (1%)

Query: 2   SLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDI 61
           S +L L+ I K +PGV+AL+ VSL +  GEVHAL+GENGAGKSTL+KV+ G    D G I
Sbjct: 5   SPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQI 64

Query: 62  LFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR-RLGLIHFKKMYAD 120
           +   +P   + P+DA+  GI  ++QE++L   L+VA+N++LG  PR R GL+ + ++ A 
Sbjct: 65  IVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAK 124

Query: 121 ARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLF 180
             A+L + K+  +    + D SIA QQ++ IAR + + AK ++ DEPTASL   E  VLF
Sbjct: 125 TNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLF 184

Query: 181 GILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS 240
            +++ L+ +GV I +I+H ++++++I+DRI+VLR+GQ+ G   TAE  +  + + M+GR 
Sbjct: 185 EVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRK 244

Query: 241 LQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEV 300
           L    + + E    +     V L +  +S     + +N  V +G+ VG  GL+G+GR+E+
Sbjct: 245 LD---LSRNEAHHELGE---VALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEI 298

Query: 301 CNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA 360
              +FGL    SGSI L G ++ ++ P DAI  GI+L PEDRK  G++  ++ R+N+ L 
Sbjct: 299 AETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLP 358

Query: 361 LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI 420
               +    ++++  +  I   + DKL I TP   + +  LSGGNQQK+++ +WL++ P 
Sbjct: 359 QVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPN 418

Query: 421 LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVR 480
           +L++DEPTRGID+G+ AEI  L+R L  +G +++V SSE+ E++  ++++V +     +R
Sbjct: 419 VLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMR 478

Query: 481 ELSGAELTSQHVMQAIA 497
             +  E+T ++++ AI+
Sbjct: 479 TFTSEEVTEENLIAAIS 495



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 66/249 (26%), Positives = 116/249 (46%), Gaps = 23/249 (9%)

Query: 6   ELKQISKHYPGVKA---LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62
           EL +++    G+      EDV+  +  GEV    G  GAG++ + + + G ++   G I 
Sbjct: 255 ELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIF 314

Query: 63  FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPR------RLGLIHFKK 116
             G      +P DA + GIS       LVP     Q L LG   R      ++  +    
Sbjct: 315 LDGAEVAITSPHDAIERGIS-------LVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGP 367

Query: 117 MYADAR--AVLTQFKLDIDVSAP-----LSDYSIAVQQLIAIARGVAMSAKVLVLDEPTA 169
             AD    A+  Q++  +D+  P     + + S   QQ I I + ++M   VL++DEPT 
Sbjct: 368 FVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTR 427

Query: 170 SLDAKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQ 229
            +D      +  +L  L A+G A++ I+  + +V  ++DRI  + +G+ +  + + E+ +
Sbjct: 428 GIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTE 487

Query: 230 PKLIEAMLG 238
             LI A+ G
Sbjct: 488 ENLIAAISG 496


Lambda     K      H
   0.319    0.136    0.377 

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: 605
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: 499
Length of database: 503
Length adjustment: 34
Effective length of query: 465
Effective length of database: 469
Effective search space:   218085
Effective search space used:   218085
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
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