GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Sinorhizobium meliloti 1021

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate SMc02739 SMc02739 glycine betaine transport ATP-binding ABC transporter protein

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__Smeli:SMc02739
          Length = 349

 Score =  265 bits (677), Expect = 2e-75
 Identities = 141/283 (49%), Positives = 194/283 (68%), Gaps = 4/283 (1%)

Query: 1   MAIKLEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIM 60
           M+  +  KN+  IFG++PQ A + ++QG ++++I   TGL LGV  ASL I EGEI V+M
Sbjct: 1   MSDAVVFKNVDIIFGKNPQLAVQMVDQGKTRDEIGAATGLVLGVAGASLTINEGEILVLM 60

Query: 61  GLSGSGKSTMVRLLNRLIEPTRGQVLID----GVDIAKISDAELREVRRKKIAMVFQSFA 116
           GLSGSGKST++R +N L    RG+V +      ++  + +   LR+ R   ++MVFQ FA
Sbjct: 61  GLSGSGKSTLLRAVNGLAPVVRGEVEVKTANGSLNPYRCNAKSLRDFRMHTVSMVFQQFA 120

Query: 117 LMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLA 176
           L+P  TV DN  FG+ELAG+   ERR++  + L  V L  +A    +ELSGGM+QRVGLA
Sbjct: 121 LLPWRTVADNVGFGLELAGVADAERRKRVGEQLELVNLAKWADRKVNELSGGMQQRVGLA 180

Query: 177 RALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIA 236
           RA A    ILLMDE FSALDPLIRT +QDEL++ Q + ++TI+F+SHDLDEA RIG+RIA
Sbjct: 181 RAFATGAPILLMDEPFSALDPLIRTRLQDELLEFQRRLKKTIIFVSHDLDEAFRIGNRIA 240

Query: 237 IMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDI 279
           IM+ G ++Q GTP EI+  PAN YV  F + ++   + +AKD+
Sbjct: 241 IMEGGRIIQCGTPQEIVKKPANQYVADFVQHMNPITMLTAKDV 283


Lambda     K      H
   0.319    0.137    0.378 

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: 393
Number of extensions: 12
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: 1
Length of query: 400
Length of database: 349
Length adjustment: 30
Effective length of query: 370
Effective length of database: 319
Effective search space:   118030
Effective search space used:   118030
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: 50 (23.9 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