GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Desulfovibrio vulgaris Miyazaki F

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 8500413 DvMF_1163 ABC transporter related (RefSeq)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__Miya:8500413
          Length = 255

 Score =  245 bits (626), Expect = 6e-70
 Identities = 121/251 (48%), Positives = 172/251 (68%)

Query: 4   PILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63
           P+LE+ G+T RFGGL AV+  N+ +EE++++++IGPNGAGKTTVFN ++GFYQPT G I 
Sbjct: 2   PLLEMKGVTQRFGGLQAVSDFNISLEERKLIALIGPNGAGKTTVFNLVSGFYQPTEGQII 61

Query: 64  LDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAF 123
            DG+   GL  H++  +G+ RTFQN+RL+ EM+ ++N+ +AQH  L         +T  F
Sbjct: 62  FDGKPTAGLRPHQVTARGIARTFQNIRLWHEMSVLDNIRIAQHHRLGYTIWDAFLRTGRF 121

Query: 124 RRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183
            RSE      A   LE ++L + A+     L YG QRR+EIAR M  RP++L+LDEPAAG
Sbjct: 122 TRSEGNIDTIAWEMLEAMDLKDAAHELPRNLPYGLQRRVEIARAMSIRPKLLLLDEPAAG 181

Query: 184 LNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRD 243
           LN  + D L  LI  +  E ++ + +IEH MK+VMS+ + I VI+ G+ +A+GTPE+I+ 
Sbjct: 182 LNSADVDGLIKLIRWIHDEFDIAIWMIEHQMKVVMSLCEWIKVIDFGSTIAEGTPEEIQS 241

Query: 244 NPDVIKAYLGE 254
           NP VIKAYLG+
Sbjct: 242 NPVVIKAYLGD 252


Lambda     K      H
   0.320    0.137    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: 203
Number of extensions: 8
Number of successful extensions: 1
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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: 47 (22.7 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