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 ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate 8500738 DvMF_1481 ABC transporter related (RefSeq)

Query= uniprot:A0A159ZWS6
         (255 letters)



>FitnessBrowser__Miya:8500738
          Length = 259

 Score =  226 bits (577), Expect = 3e-64
 Identities = 110/249 (44%), Positives = 161/249 (64%), Gaps = 1/249 (0%)

Query: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64
           +L V +LS+ FGG+ A++  + T +   + ALIGPNGAGKTT+ NC+TG  +P  G +  
Sbjct: 3   LLAVRDLSVAFGGIRALDAASFTAQAGAITALIGPNGAGKTTLVNCVTGMVRPDSGNVAF 62

Query: 65  DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124
           DG  I G+  H + R G+ RTFQ++R+F  M+ +EN+++  H H+ T   + + + P  R
Sbjct: 63  DGRDITGMAAHRLPRLGLARTFQHLRVFGSMSLLENVMVGLHGHVRTGMLSSMLRLPGVR 122

Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
           ++ER   + A   LD   L + A+  AG L YG Q+RL +AR ++  PR+++LDEP AGL
Sbjct: 123 RTERAMRDAAMRALDFTGLADRADGAAGLLPYGDQKRLVLARALVGDPRMILLDEPVAGL 182

Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDN 244
           NP ET ++  LI  LR    V VLLIEHDM LVM +SD +VV+  G  +A+G P +++ N
Sbjct: 183 NPAETHEMGGLILALR-ARGVAVLLIEHDMSLVMRVSDAVVVLCSGAKIAEGAPGEVKRN 241

Query: 245 PEVIKAYLG 253
           PEV+ AYLG
Sbjct: 242 PEVVNAYLG 250


Lambda     K      H
   0.321    0.138    0.398 

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: 197
Number of extensions: 5
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: 255
Length of database: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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