Alignments for a candidate for araG in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Rhodobacter viridis JA737

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_110805317.1 C8J30_RS07980 ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_003217355.1:WP_110805317.1
          Length = 505

 Score =  251 bits (640), Expect = 6e-71
 Identities = 157/482 (32%), Positives = 257/482 (53%), Gaps = 21/482 (4%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L   G+ K +PGV A   + F+   G+VHAL+GENGAGKSTL+K++ G   P  G +   
Sbjct: 6   LKIEGLTKAYPGVVANDGVGFEVAPGEVHALLGENGAGKSTLVKMIYGLVKPDAGRMTFQ 65

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG--QLPHKGGIVNRSLLNYEAG 125
           G+  + ++  AA  AGVA+++Q   L   + VAEN+ LG    P  G +  R      A 
Sbjct: 66  GRPYTPAEPRAARAAGVAMVFQHFSLFEALNVAENVALGMENPPPMGDLAERIRAISTA- 124

Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185
                 G+ +DP   +  LS G+ Q VEI + L ++ K++  DEPTS L+ +E++ LF  
Sbjct: 125 -----YGLPLDPARTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFHT 179

Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245
           +R+L  EG  ILY+SH++EEI +L D  T+ + G+ V +    ++   + L + MVG + 
Sbjct: 180 LRKLAAEGTAILYISHKLEEIRSLCDGATILRGGKVVASCIPREKSARE-LAELMVGGEF 238

Query: 246 G--DIYGWQPRSYGEERLRLDAVKAPGVR------TPISLAVRSGEIVGLFGLVGAGRSE 297
              D  G   R  G   L +D +  P +         +S ++ +GE++G+ G+ G G+ E
Sbjct: 239 AATDRAG---RVSGATILEVDHLNLPPMTQFGPALKNVSFSLAAGEVLGIGGVAGNGQEE 295

Query: 298 LMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINI 357
           L+  + G     AG V +  Q I    P+     G++  PE+R     +P  S+ +N  +
Sbjct: 296 LLATLSGERPSGAGTVSLHGQDISDLGPNDRRRLGLLAAPEERLGHAAVPNLSLTENAIL 355

Query: 358 SAR-RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSE 416
           +   R+ +     +N G     A+  I+  +++TPG       LSGGN QK ++GR + +
Sbjct: 356 TGTVRRPLTRNGFLNMGAARRFAEEIIKGFDVRTPGPHVAARALSGGNLQKFVIGREVLQ 415

Query: 417 EMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGE 476
             +V+++++PT G+D  A   I   +  LAA+G AV+  S DL E++ +ADR   + EG 
Sbjct: 416 SPEVLVVNQPTWGVDAAAAAAIRQSLLDLAAKGAAVIVISQDLDELMEIADRFCALNEGR 475

Query: 477 IA 478
           ++
Sbjct: 476 LS 477



 Score = 69.7 bits (169), Expect = 2e-16
 Identities = 53/231 (22%), Positives = 105/231 (45%), Gaps = 19/231 (8%)

Query: 269 PGV--RTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPS 326
           PGV     +   V  GE+  L G  GAG+S L+K ++G  +  AG++    +P    +P 
Sbjct: 16  PGVVANDGVGFEVAPGEVHALLGENGAGKSTLVKMIYGLVKPDAGRMTFQGRPYTPAEPR 75

Query: 327 HAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSL 386
            A AAG+ +  +      +    +V +N+ +       +G                IR++
Sbjct: 76  AARAAGVAMVFQHFS---LFEALNVAENVALGMENPPPMGDLA-----------ERIRAI 121

Query: 387 NIKTP---GAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIY 443
           +          + + +LS G +Q+  + R L ++ K++++DEPT  +       +++ + 
Sbjct: 122 STAYGLPLDPARTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFHTLR 181

Query: 444 ALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSL 494
            LAA+G A+L+ S  L E+  + D   ++R G++    +  +   R+   L
Sbjct: 182 KLAAEGTAILYISHKLEEIRSLCDGATILRGGKVVASCIPREKSARELAEL 232


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: 616
Number of extensions: 38
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: 504
Length of database: 505
Length adjustment: 34
Effective length of query: 470
Effective length of database: 471
Effective search space:   221370
Effective search space used:   221370
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 24 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 2024 update 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