GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Desulfovibrio vulgaris Miyazaki F

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  254 bits (648), Expect = 7e-72
 Identities = 157/490 (32%), Positives = 262/490 (53%), Gaps = 12/490 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +++  GI K F  V A  ++  ++    I +L+GENGAGKSTL+ IL G L+ DAG I+V
Sbjct: 29  VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
           +G    F SP DA + GI +++Q   L D+MTVAEN+ L      GQ   +  R     M
Sbjct: 89  DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLL------GQSPDMLLRPAR--M 140

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
                 L +  G    P A V  L+  +RQ VEI K L ++ R++ +DEPT+ LT  ET+
Sbjct: 141 RDEVAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETD 200

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII-KMM 252
           +LFE +  +  +G ++VF+SH+L EV+ ++D I ++R G+ + E  + +    T++   M
Sbjct: 201 QLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRM 260

Query: 253 VGREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312
           VGR+V          P +  L V +L     + +VS +VR+GE++  AG+ G G+ E + 
Sbjct: 261 VGRDVVLQVDAKRLTPVDTVLSVEHLSGAG-LSDVSLQVRRGEIVAIAGVAGNGQKELVE 319

Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372
            + G+ + E+G++ + GR           + G+  IPEDR+       + + DN +L + 
Sbjct: 320 AICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTR 379

Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432
            + ++ G+ LD  +     +  V   +++   I      LSGGN QK+V+ +      ++
Sbjct: 380 NQFAK-GVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEV 438

Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492
           ++ + PT+G+D+ A  E+   + E A     V++++ +L E L L+DRI VM+ G    V
Sbjct: 439 IVAENPTQGLDISATEEVWGRLLE-ARSTSGVLLVTGDLNEALELADRIAVMYRGRFIDV 497

Query: 493 LDNREKRVTQ 502
            D  +    Q
Sbjct: 498 FDKDDTAKVQ 507


Lambda     K      H
   0.319    0.138    0.381 

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: 624
Number of extensions: 33
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 520
Length of database: 537
Length adjustment: 35
Effective length of query: 485
Effective length of database: 502
Effective search space:   243470
Effective search space used:   243470
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:

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