GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Pseudomonas stutzeri RCH2

Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= SwissProt::P0AER3
         (246 letters)



>FitnessBrowser__psRCH2:GFF3103
          Length = 394

 Score = 96.7 bits (239), Expect = 6e-25
 Identities = 65/176 (36%), Positives = 98/176 (55%), Gaps = 15/176 (8%)

Query: 71  LFRNVPLIVQF-----FTWYLVIPELLPEKI-GMWFKAELDPNIQFFLSSMLCLGLFTAA 124
           LF  +P ++ F     FTW   +PEL    I G W        I   +S ++ L ++TAA
Sbjct: 224 LFLAIPWLMTFIAGAPFTWE--VPELQRFNIRGGWVV------IPELVSIVVALSVYTAA 275

Query: 125 RVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSA 184
            + E VR+ IQS+  GQ  AA ++GL   Q  R V++P A RVIVPP+TS+ +NL KNS+
Sbjct: 276 FIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLVIVPQALRVIVPPLTSQYLNLAKNSS 335

Query: 185 IASTIGLVDMAAQ-AGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRL 239
           +A+ IG  DM +  AG +L+ +  A E+       Y+ I+  I L+M    +++ L
Sbjct: 336 LAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSVYLAISISISLLMNWYNKRIAL 391



 Score = 49.3 bits (116), Expect = 1e-10
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 20  TYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNRFLSGLGTLYVELFRNV-PLI 78
           TY    W G   T+ +S+    +A ++G   G+ R   N  +  L TLY+E+FRN+ PL+
Sbjct: 80  TYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIPPLL 139

Query: 79  VQFFTWYLVIPEL 91
           + FF ++ VI  L
Sbjct: 140 LIFFVYFAVISPL 152


Lambda     K      H
   0.328    0.140    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: 265
Number of extensions: 20
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 246
Length of database: 394
Length adjustment: 27
Effective length of query: 219
Effective length of database: 367
Effective search space:    80373
Effective search space used:    80373
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: 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