GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Herbaspirillum seropedicae SmR1

Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate HSERO_RS16725 HSERO_RS16725 ABC transporter permease

Query= reanno::Smeli:SM_b21653
         (298 letters)



>FitnessBrowser__HerbieS:HSERO_RS16725
          Length = 299

 Score =  125 bits (313), Expect = 2e-33
 Identities = 92/283 (32%), Positives = 140/283 (49%), Gaps = 11/283 (3%)

Query: 13  DVNGWLFVAPALGLITLFMVYPIAWSLWMSFQSGR-GMTLKFAGFANIVRLWNDPVFIKA 71
           +V G LF+APA+ L+ +F+ YP+   +W+ F   + G    F G  N   L  D +   +
Sbjct: 10  NVLGMLFMAPAVILLVVFLTYPLGLGIWLGFTDTKIGGEGSFIGLDNFTYLAGDSLAQLS 69

Query: 72  LTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMF 131
           L NT+ Y V    +  +L L LA LLN   +  +  FR  + LP +      ++ F  ++
Sbjct: 70  LFNTVFYTVSASILKFMLGLWLAILLNK-NVPLKTFFRAIVLLPWIVPTALSALAFWWLY 128

Query: 132 -ATDGIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKS 190
            A   +++  L  +GL    I +L  P+ A+   + A  WR   +  I  LA LQ I  S
Sbjct: 129 DAQFSVISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLAGLQTISPS 188

Query: 191 IYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNAT 250
           +YE A IDG   W +  H+T+PLL P+I      S + T   F  +Y LT  +GGP NAT
Sbjct: 189 LYEAAAIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLT--RGGPLNAT 246

Query: 251 LTLSLYIYNLTFRFMPN--LGY-AATVSYVIVVLVALLAFVQF 290
             ++   +    R +P   LG  AA  +Y+I  L+A + F  F
Sbjct: 247 HLMATLSFQ---RAIPGGALGEGAALATYMIPFLLAAIMFSYF 286


Lambda     K      H
   0.330    0.142    0.447 

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: 285
Number of extensions: 14
Number of successful extensions: 3
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: 298
Length of database: 299
Length adjustment: 27
Effective length of query: 271
Effective length of database: 272
Effective search space:    73712
Effective search space used:    73712
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 (21.9 bits)
S2: 48 (23.1 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