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 SMc00771 SMc00771 putrescine ABC transporter ATP-binding protein

Query= CharProtDB::CH_001555
         (400 letters)



>FitnessBrowser__Smeli:SMc00771
          Length = 381

 Score =  191 bits (484), Expect = 4e-53
 Identities = 117/289 (40%), Positives = 172/289 (59%), Gaps = 15/289 (5%)

Query: 29  LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88
           +S + + +K G    V D SL I   E F ++G SG GKST++R+L    +PT G++++D
Sbjct: 24  ISVKNVTKKFGDFTAVDDLSLNIYTREFFALLGASGCGKSTLLRMLAGFEQPTSGEIILD 83

Query: 89  GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDA 148
           G  +A I         R+ + M+FQS+AL PHMTV +N AFG++  G+   +  E+    
Sbjct: 84  GQSLAGIPPY------RRPVNMMFQSYALFPHMTVENNVAFGLKQDGMPKADIAERVAQM 137

Query: 149 LRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELV 208
           L+ V LE +A   P +LSGG RQRV LAR+LA  P +LL+DE   ALD  +R E Q EL+
Sbjct: 138 LKLVKLEKFAKRKPHQLSGGQRQRVALARSLAKRPKVLLLDEPLGALDKKLREETQFELM 197

Query: 209 KLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268
            LQ +   T V ++HD +EAM + DRIA+M +G+VVQV TP EI   P + +V  F   V
Sbjct: 198 DLQQELGLTFVVVTHDQEEAMTMADRIAVMSHGKVVQVATPAEIYEAPNSRFVADFIGDV 257

Query: 269 DI--SQVFSAKD--IARRTPNGL-IR----KTPGFGPRSALKLLQDEDR 308
           +I   +V SA+D  I   T  G+ +R    + PG G ++A+ +  ++ R
Sbjct: 258 NIFDGKVTSAEDGYIRVETTGGIPVRMASPEKPGNGAKAAVAIRPEKIR 306


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: 327
Number of extensions: 13
Number of successful extensions: 2
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: 400
Length of database: 381
Length adjustment: 31
Effective length of query: 369
Effective length of database: 350
Effective search space:   129150
Effective search space used:   129150
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