GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Desulfovibrio vulgaris Hildenborough

Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate 209488 DVU0549 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= SwissProt::P22729
         (425 letters)



>lcl|MicrobesOnline__882:209488 DVU0549 high-affinity branched-chain
           amino acid ABC transporter, permease protein
          Length = 407

 Score =  323 bits (829), Expect = 5e-93
 Identities = 165/314 (52%), Positives = 219/314 (69%), Gaps = 20/314 (6%)

Query: 93  LVALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYT 152
           L+A+LV+    P +VS    +I    ++Y++LGLGLN+VVGLSG LVLGY  FYA+GAY 
Sbjct: 93  LLAVLVVFAVLPMLVSTYQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYA 152

Query: 153 FALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNN 212
           +ALLN  +GLGFWT LPI G +AA  G LLGFPVLRL+GDYLAIVTLGFGEIVR++L N 
Sbjct: 153 YALLNADFGLGFWTVLPIGGALAAVFGILLGFPVLRLKGDYLAIVTLGFGEIVRLVLENW 212

Query: 213 TEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLV 272
             +T GP+GIS+I +P LFG+E S                     S+   ++Y + L  V
Sbjct: 213 GSVTRGPSGISKIARPGLFGMELS--------------------VSEATTYIYYLILAAV 252

Query: 273 VLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAA 332
           + ++F + RL    +GRAW+ALREDEIAC ++G+     KLTAF + A +AGFAG +FAA
Sbjct: 253 IFTIFAVGRLKDSRIGRAWQALREDEIACEAMGIDLTTTKLTAFALGACWAGFAGVIFAA 312

Query: 333 RQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLGG 392
           +  F++P SFTF ESA +LA+VVLGGMGS   V+L A++L++  E +R F+EY ML+ G 
Sbjct: 313 KTTFINPASFTFLESAMILAMVVLGGMGSTLGVVLGALVLILLPEYLRAFSEYRMLIFGA 372

Query: 393 LMVLMMIWRPQGLL 406
            MVLMM++RPQGL+
Sbjct: 373 AMVLMMVFRPQGLV 386


Lambda     K      H
   0.330    0.145    0.436 

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: 390
Number of extensions: 10
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: 425
Length of database: 407
Length adjustment: 31
Effective length of query: 394
Effective length of database: 376
Effective search space:   148144
Effective search space used:   148144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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