GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsA in Sinorhizobium meliloti 1021

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate SMc04259 SMc04259 periplasmic binding ABC transporter signal peptide protein

Query= reanno::WCS417:GFF4324
         (428 letters)



>lcl|FitnessBrowser__Smeli:SMc04259 SMc04259 periplasmic binding ABC
           transporter signal peptide protein
          Length = 411

 Score =  218 bits (554), Expect = 4e-61
 Identities = 127/347 (36%), Positives = 179/347 (51%), Gaps = 10/347 (2%)

Query: 7   LAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAG 66
           LA A+   +  P   F A S   +EV HWWTSGGE AAV  L    +  G  W DGA+AG
Sbjct: 6   LAAALGATAALP---FGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAG 62

Query: 67  GGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKWDSLLD- 124
            GG TA  ++ SR   G+P    Q   G   +E    GL+    L D+A +E W  ++  
Sbjct: 63  SGG-TARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRD--LTDIATKENWKEIVKP 119

Query: 125 KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGF 184
             + D+   EG     PVNIH   WLW++   FK+AG+ + P    EF AA   L+ AG 
Sbjct: 120 SSLLDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGV-EVPKNWDEFVAAAPALEKAGI 178

Query: 185 IPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYM 244
           +PLA GGQPWQ +  F+ +++++ G + ++K     D     GPE+ K        A  M
Sbjct: 179 VPLAVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADD-ARRM 237

Query: 245 DVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYN 304
                 QDWN     VI GKAG QIMGDWA+ E+  A + AG DY C+   G ++  +  
Sbjct: 238 SKGTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTG 297

Query: 305 IDSLAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDM 351
            D+      +D+  +  Q+ +A  +L    Q  F++ KGS+PVR D+
Sbjct: 298 GDAFYFPLLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDV 344


Lambda     K      H
   0.314    0.131    0.388 

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: 520
Number of extensions: 27
Number of successful extensions: 4
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: 428
Length of database: 411
Length adjustment: 32
Effective length of query: 396
Effective length of database: 379
Effective search space:   150084
Effective search space used:   150084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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