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 GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  262 bits (670), Expect = 2e-74
 Identities = 169/479 (35%), Positives = 255/479 (53%), Gaps = 15/479 (3%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +L L+ I+K +  V A +DVS  LF GEV ALLGENGAGK+TL+ ++ G    D G +  
Sbjct: 15  VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGL-IHFKKMYADAR 122
            G P     P  A   G+  V+Q   L  NLTV +N+ LG EP  LGL +      A  R
Sbjct: 75  FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEP-LLGLGLRAGPAKARIR 133

Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
           A+  QF L +D +A +S  ++  +Q + I + +   A++L+LDEPTA L  +E   LF  
Sbjct: 134 ALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFAT 193

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           L +   +G++++FI+H L +V  ISDR+ VLR+G+ + E  TA+     L   M+G    
Sbjct: 194 LREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVG---- 249

Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGS-----IQSMNLTVPKGQAVGLAGLLGSGR 297
               D    +         LL L DV+   +     ++ ++L +  GQ  GLAG+ G+G+
Sbjct: 250 ---ADVVPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQ 306

Query: 298 SEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI 357
           + + + V GL    SGS+ L G       P +AI+AGIA  PEDR   G I    + EN 
Sbjct: 307 AALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENA 366

Query: 358 ILALQA-RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLA 416
           IL   A R     +L     ++ A+  I    +  P  D  I  LSGGN QK+IL R L 
Sbjct: 367 ILETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLE 426

Query: 417 IEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRD 475
             P +++ ++P RG+DIGA   + + +   C  G ++L+ S +LDE++  S+ + V+ +
Sbjct: 427 QSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISE 485



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 54/208 (25%), Positives = 104/208 (50%), Gaps = 10/208 (4%)

Query: 284 GQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRK 343
           G+ + L G  G+G++ + N +FG  + D+G + L G  L    P  A+  G+ +  +   
Sbjct: 41  GEVIALLGENGAGKTTLMNILFGQYMADTGGVELFGAPLPPGAPRAALDGGVGMVHQHFT 100

Query: 344 IDGIIGPLSIRENIILALQARIGWWRYL--SNTRQQEIAQFFIDKLQIATPDADKPIEQL 401
           +      L++ ENI L ++  +G       +  R + +A+ F  K+     D +  + +L
Sbjct: 101 L---ADNLTVWENITLGVEPLLGLGLRAGPAKARIRALAEQFHLKV-----DPNAKVSRL 152

Query: 402 SGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELD 461
           + G +Q+V + + L  +  +L+LDEPT  +       +   +R   + G+S++  S +L 
Sbjct: 153 TVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATLREAINRGLSVIFISHKLH 212

Query: 462 ELVAFSNKVVVLRDRYAVRELSGAELTS 489
           E++A S++V+VLR    V E   A+  S
Sbjct: 213 EVMAISDRVLVLRHGKLVAERQTADTDS 240



 Score = 67.0 bits (162), Expect = 2e-15
 Identities = 55/226 (24%), Positives = 107/226 (47%), Gaps = 16/226 (7%)

Query: 4   ILELKQISKHYPGVK-ALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62
           +L+L+ ++    G    L  VSL L AG++  L G +G G++ L  +++G  +   G + 
Sbjct: 266 LLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLVSGLITPQSGSLT 325

Query: 63  FLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEPRRL---GLIHFKK 116
             G      +P +A  AGI+ + ++      + +  + +N  L     R    G + ++ 
Sbjct: 326 LNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETYATRFSHRGWLDWRA 385

Query: 117 MYADARAVLTQFKLDIDVSAPLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASL 171
               A+ V+T +    DV  P  D  I +      Q + + R +  S ++++ ++P   L
Sbjct: 386 ARDFAKTVITGY----DVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQIILANQPVRGL 441

Query: 172 DAKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQ 217
           D   V  +   L +  A+G A++ I+  LD++ Q+SD I V+  G+
Sbjct: 442 DIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGR 487


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: 575
Number of extensions: 32
Number of successful extensions: 8
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: 499
Length of database: 522
Length adjustment: 34
Effective length of query: 465
Effective length of database: 488
Effective search space:   226920
Effective search space used:   226920
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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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