GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_068169394.1 HTA01S_RS08705 branched-chain amino acid ABC transporter permease

Query= SwissProt::P22729
         (425 letters)



>NCBI__GCF_001592305.1:WP_068169394.1
          Length = 333

 Score =  150 bits (379), Expect = 6e-41
 Identities = 105/344 (30%), Positives = 174/344 (50%), Gaps = 30/344 (8%)

Query: 72  VSGPKFILPAIDGSTVKQKLFLVALLVLAVAWPFMVSRGT---VDIATLTMIYIILGLGL 128
           +S PK  L  +  S   Q L  +  + LA A+P + S      + + +  MI  I  + L
Sbjct: 1   MSSPKAQLEKLPRSV--QVLLALGAVALA-AFPLVPSDSADFYLQMLSQMMILAIFAMSL 57

Query: 129 NVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYG-LGFWTCLPIAGLMAAAAGFLLGFPVL 187
           +++ G+SGL+ LG+  ++ +  Y  A L      +  W  LP++ L A  A  ++GF V+
Sbjct: 58  DLLQGVSGLVSLGHAAYFGLAGYALAFLTPADAPISLWWALPVSALGAGLAALVIGFFVV 117

Query: 188 RLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNG--ISQIPKPTLFGLEFSRTAREGGWD 245
           R  G Y  +VT+ F ++V  L  +N E+ GG +G  ++  P  TLFG             
Sbjct: 118 RTHGIYFIMVTMAFAQMVFFLFFDNKEL-GGSDGLYVNFRPDATLFG------------- 163

Query: 246 TFSNFFGLKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLG 305
               + G+  D  ++  F Y    +LV +  F + RLL  P GR    +R +E   R++G
Sbjct: 164 ----WAGI--DLENKTTFYYFTLAMLVAVYAF-LRRLLFSPFGRVLAGIRVNEHRMRAVG 216

Query: 306 LSPRRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAV 365
                 KL AFT++   AG AG L+AA+ GFV+P+   F  SA  + +V+LGGMG+    
Sbjct: 217 YGTFGYKLAAFTLAGTLAGVAGFLWAAQTGFVNPDLMGFHMSAHAIMMVILGGMGNFAGA 276

Query: 366 ILAAILLVVSRELMRDFNEYSMLMLGGLMVLMMIWRPQGLLPMT 409
           I+ A          +D  ++  L++G  +VL++++ P+GLL ++
Sbjct: 277 IVGAFAFEYVMHFFKDLTKHWQLLMGSFIVLVVVFAPRGLLGLS 320


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: 284
Number of extensions: 8
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: 333
Length adjustment: 30
Effective length of query: 395
Effective length of database: 303
Effective search space:   119685
Effective search space used:   119685
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 Apr 09 2024. 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