GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5405 in Sinorhizobium meliloti 1021

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate SMc03135 SMc03135 amino-acid transport system ATP-binding ABC transporter protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>lcl|FitnessBrowser__Smeli:SMc03135 SMc03135 amino-acid transport
           system ATP-binding ABC transporter protein
          Length = 251

 Score =  382 bits (980), Expect = e-111
 Identities = 182/245 (74%), Positives = 213/245 (86%), Gaps = 2/245 (0%)

Query: 10  SPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69
           SPE  I + GV+KWYGQ+H L DINL++   E++V+CGPSGSGKST IRC+NRLE HQQG
Sbjct: 9   SPE--ITLSGVHKWYGQYHALDDINLSIASREKVVICGPSGSGKSTLIRCVNRLEAHQQG 66

Query: 70  RIVVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEI 129
           RIVV GVE+  D ++++AIRREVGMVFQ FNLFPHLTIL+NC LAPMWV++MP+ +A EI
Sbjct: 67  RIVVGGVEVGEDERKVDAIRREVGMVFQQFNLFPHLTILENCILAPMWVKRMPRAQATEI 126

Query: 130 AMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVL 189
           AM YL RVRIPEQA+KYPGQLSGGQQQRVAIARALCM PK+MLFDEPTSALDPEMVKEVL
Sbjct: 127 AMDYLNRVRIPEQANKYPGQLSGGQQQRVAIARALCMNPKVMLFDEPTSALDPEMVKEVL 186

Query: 190 DTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFL 249
           DTM+ LA DGMTM+CVTHEMGFAR VA+RVIFMD+G IVE+  P++FF +P+ DR  LFL
Sbjct: 187 DTMVALANDGMTMVCVTHEMGFARQVADRVIFMDQGRIVEEGEPDEFFAHPKTDRASLFL 246

Query: 250 SQILH 254
           SQ+LH
Sbjct: 247 SQLLH 251


Lambda     K      H
   0.322    0.137    0.407 

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: 275
Number of extensions: 7
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: 254
Length of database: 251
Length adjustment: 24
Effective length of query: 230
Effective length of database: 227
Effective search space:    52210
Effective search space used:    52210
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 (21.9 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 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