GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Herbaspirillum seropedicae SmR1

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate HSERO_RS08290 HSERO_RS08290 leucine/isoleucine/valine transporter ATP-binding subunit

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__HerbieS:HSERO_RS08290
          Length = 234

 Score =  297 bits (761), Expect = 1e-85
 Identities = 155/235 (65%), Positives = 185/235 (78%), Gaps = 1/235 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           ML+   VHT YGAIEAL GV + +  GEIV+LIGANGAGK+TLLMT+CG PRA  GR+ F
Sbjct: 1   MLQFDKVHTHYGAIEALHGVSLNVEKGEIVTLIGANGAGKTTLLMTLCGRPRASSGRVIF 60

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120
           EGQDITQ+ T+E++R G+A SPEGRR+FP ++VLENL+MG+  A   +    +E V  LF
Sbjct: 61  EGQDITQLQTHEIMRRGLAISPEGRRVFPSLTVLENLKMGAFFASNEAIEQGIEYVFGLF 120

Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180
           PRLKER +QRAGTMSGGEQQMLAIGRALMS+PRLLLLDEP+LGLAPLV+ QIF  ++ I 
Sbjct: 121 PRLKERAAQRAGTMSGGEQQMLAIGRALMSKPRLLLLDEPTLGLAPLVIAQIFDIIRTI- 179

Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEGG 235
           RE  +TVF+VEQNA  AL +A RGYV+ NG V MS TGA LLAN +VR AYL  G
Sbjct: 180 RESGVTVFLVEQNANKALGVADRGYVLENGHVVMSDTGANLLANSDVRKAYLGHG 234


Lambda     K      H
   0.320    0.136    0.377 

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: 216
Number of extensions: 4
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: 236
Length of database: 234
Length adjustment: 23
Effective length of query: 213
Effective length of database: 211
Effective search space:    44943
Effective search space used:    44943
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: 46 (22.3 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