GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Desulfovibrio vulgaris Miyazaki F

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  122 bits (305), Expect = 2e-32
 Identities = 77/223 (34%), Positives = 123/223 (55%), Gaps = 11/223 (4%)

Query: 5   PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64
           P++   G+ K +G+V A      D+ PG I A++G+NGAGKS+++  ++G +  D G I 
Sbjct: 28  PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87

Query: 65  LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124
           ++G P  F SP +A +AGI  VYQ+  L  ++++A+N+ LG   + P ++      L  A
Sbjct: 88  VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLG---QSPDML------LRPA 138

Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184
            M  +  A     GL    +    V  LS G+RQ V + +     S+V+I+DEPTA L  
Sbjct: 139 RMRDEVAALAERYGLAV--DPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTP 196

Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLG 227
           +E+ ++ E +  +  +G  +V ISH +  V  VAD I I R G
Sbjct: 197 RETDQLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRG 239



 Score = 73.6 bits (179), Expect = 8e-18
 Identities = 61/226 (26%), Positives = 99/226 (43%), Gaps = 12/226 (5%)

Query: 32  GEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ--FRSPMEAR-QAGIETVYQ 88
           GEI+A+ G  G G+  +++AI G   P+ GE+R+ G+P +  F  P   R  A I    Q
Sbjct: 301 GEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQ 360

Query: 89  NLALSPALSIADNMFL-GREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQ 147
            LA    L + DN  L  R     G+       LDR       +  + E  +    +I  
Sbjct: 361 GLATCRHLDLVDNFLLTTRNQFAKGVF------LDRTEATNAVKRVVWEYNVQP-GDITA 413

Query: 148 AVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLPIVLI 207
               LSGG  Q + + R      +V++ + PT  L +  +  V   +L+ R     ++L+
Sbjct: 414 PARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GVLLV 472

Query: 208 SHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGAKEP 253
           + ++    E+ADRI +   GR + V +  D     A+  M     P
Sbjct: 473 TGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMMAGVRP 518


Lambda     K      H
   0.321    0.136    0.383 

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: 309
Number of extensions: 15
Number of successful extensions: 3
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: 260
Length of database: 537
Length adjustment: 30
Effective length of query: 230
Effective length of database: 507
Effective search space:   116610
Effective search space used:   116610
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: 49 (23.5 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:

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:

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:

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:

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