GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17600 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate AO356_05505 AO356_05505 amino acid ABC transporter permease

Query= uniprot:A0A1N7U128
         (237 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05505
          Length = 236

 Score =  339 bits (869), Expect = 3e-98
 Identities = 158/235 (67%), Positives = 203/235 (86%)

Query: 1   MIELFQQYGLAYLFSDGAGLSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVE 60
           MIEL Q+Y   +L+SDG  ++G+AMTLWL   S+++GF +SIPL++ARVS   ++RWPV+
Sbjct: 1   MIELLQEYWRPFLYSDGVNITGLAMTLWLLSASLLIGFVVSIPLSIARVSPKFYVRWPVQ 60

Query: 61  VYTYLFRGTPLYIQLLICYTGLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEI 120
            YTYLFRGTPLYIQLLICYTG+YS+  V+   +L+ FFR+A+NCT+LAF LNTCAYT EI
Sbjct: 61  FYTYLFRGTPLYIQLLICYTGIYSIAAVRAQPMLDSFFRDAMNCTILAFALNTCAYTTEI 120

Query: 121 FAGAIRNIPHGEIEAARAYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTA 180
           FAGAIR++ HGE+EAA+AYGL GW+L  +V++P+ALRR+LP YSNE+ILMLH+T++AFTA
Sbjct: 121 FAGAIRSMNHGEVEAAKAYGLTGWKLYAYVIMPSALRRSLPYYSNEVILMLHSTTVAFTA 180

Query: 181 TVADILKVARDANAETFLTFQAFGIAALLYMLLSFALVGLFRLAERRWMRFLVPT 235
           TV D+LKVARDAN+ TFLTFQ+FGIAAL+Y+ ++FALVGLFRLAERRW+ FL PT
Sbjct: 181 TVPDVLKVARDANSATFLTFQSFGIAALIYLTVTFALVGLFRLAERRWLAFLGPT 235


Lambda     K      H
   0.332    0.143    0.443 

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: 266
Number of extensions: 12
Number of successful extensions: 1
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: 237
Length of database: 236
Length adjustment: 23
Effective length of query: 214
Effective length of database: 213
Effective search space:    45582
Effective search space used:    45582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 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