GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF3103 Psest_3162 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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