GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Methanococcus aeolicus Nankai-3

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= TCDB::P0AAG3
         (241 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  140 bits (353), Expect = 2e-38
 Identities = 95/228 (41%), Positives = 137/228 (60%), Gaps = 19/228 (8%)

Query: 1   MITLKNVSKWYGHFQ----VLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQG 56
           +I  KN+ K YG  +    VL   + ++K+GE V + GPSG GKSTL+  +  L+   +G
Sbjct: 17  LIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKG 76

Query: 57  EITVDGIVVNDKKT------DLAKLRSRV-GMVFQHFELFPHLSIIENLTLAQVKVLKRD 109
            + + G     KKT      D A  R ++ G +FQ F L   L+ +EN+ L  V + +++
Sbjct: 77  MVYIKG-----KKTTMFSENDRAVFRRKISGFIFQQFNLINTLTALENVELPLV-LDEKN 130

Query: 110 KAPAREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDP 169
           K    +KA KLL+ + L    N +P QLSGGQQQRVAIARAL  +P  +  DEPT  LD 
Sbjct: 131 KNYRIKKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDS 190

Query: 170 EMINEVLDVMVEL-ANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVE 216
           +   EV+D++ EL   EG+T+++VTHE  FA K A+R+I M +G+IVE
Sbjct: 191 KNSREVMDILKELNEKEGITVIMVTHEPEFA-KYASRIINMKDGEIVE 237


Lambda     K      H
   0.320    0.135    0.383 

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: 151
Number of extensions: 9
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: 241
Length of database: 238
Length adjustment: 23
Effective length of query: 218
Effective length of database: 215
Effective search space:    46870
Effective search space used:    46870
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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