GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltL in Sinorhizobium meliloti 1021

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate SMa0489 SMa0489 ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>lcl|FitnessBrowser__Smeli:SMa0489 SMa0489 ABC transporter
           ATP-binding protein
          Length = 255

 Score =  341 bits (875), Expect = 8e-99
 Identities = 165/254 (64%), Positives = 208/254 (81%)

Query: 10  VDRSHMQVSDEIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCIN 69
           ++ + M   ++  IQ+  + K +GQF  L+ ++L V RGE+IV+ GPSGSGKST+IRCIN
Sbjct: 2   IEATFMNKPNDTMIQLIGVGKRFGQFEALKQVSLEVRRGEKIVLCGPSGSGKSTLIRCIN 61

Query: 70  RLEEHQSGKIIVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKV 129
           R+EEH SG+II+DG ELT   K+I+ VR EVGMVFQ FNLFPH+TIL+NLT+A   VRK 
Sbjct: 62  RMEEHTSGRIIIDGRELTDRTKDINAVRREVGMVFQSFNLFPHMTILKNLTIAQRLVRKT 121

Query: 130 PKREAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALD 189
           P++EA+E AM+YL++VKIPEQA KYP QLSGGQQQRVAIAR+LCMKP+IMLFDEPTSALD
Sbjct: 122 PEKEAKEVAMHYLKRVKIPEQASKYPVQLSGGQQQRVAIARALCMKPQIMLFDEPTSALD 181

Query: 190 PEMIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQ 249
           PEMI EVLD M+ LA +GMTM+CVTHEMGFA++VA+RV+FM  GQ++E+ +P  FF NP+
Sbjct: 182 PEMISEVLDVMVDLARDGMTMICVTHEMGFARSVADRVMFMDGGQLIEEGDPETFFANPR 241

Query: 250 SERTKQFLSQILGH 263
           +ERT  FL QIL H
Sbjct: 242 NERTALFLRQILRH 255


Lambda     K      H
   0.320    0.134    0.391 

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: 257
Number of extensions: 6
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: 263
Length of database: 255
Length adjustment: 24
Effective length of query: 239
Effective length of database: 231
Effective search space:    55209
Effective search space used:    55209
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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