GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Sphingomonas indica Dd16

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_085219126.1 B9N75_RS12690 ATP-binding cassette domain-containing protein

Query= TCDB::P0AAG3
         (241 letters)



>NCBI__GCF_900177405.1:WP_085219126.1
          Length = 252

 Score =  152 bits (384), Expect = 6e-42
 Identities = 89/227 (39%), Positives = 136/227 (59%), Gaps = 3/227 (1%)

Query: 2   ITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVD 61
           I +K+V+K +G   VL   S +VK GE + + G SG+GKS LIK + GL     G I +D
Sbjct: 7   IAIKDVAKAFGENVVLDGVSLDVKTGESLAIIGQSGTGKSVLIKCILGLLTPDAGSIRID 66

Query: 62  G-IVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKL 120
           G  VV   + +  ++R + GM+FQ   LF  L I  N+T    +   ++ A  R+ A + 
Sbjct: 67  GQEVVGASEREQERIRRKTGMLFQGGALFDSLPIWRNVTFGLTRGAYKNPAKMRDIAAEN 126

Query: 121 LERVGLSAH-ANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVM 179
           LERVGL A   +  P+ LSGG Q+RVA+ARA+   P  + FDEPT+ LDP   + + D++
Sbjct: 127 LERVGLGADILDLRPSALSGGMQKRVALARAVAPRPEILFFDEPTTGLDPIRADVINDLI 186

Query: 180 VELANE-GMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFD 225
           + L ++ G+T + +TH+M  ARK+A+RV  +  G+I+   P+D  +D
Sbjct: 187 MSLVDDLGITALTITHDMASARKIAHRVAMLYRGRIIWCGPRDRLYD 233


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: 143
Number of extensions: 12
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: 252
Length adjustment: 24
Effective length of query: 217
Effective length of database: 228
Effective search space:    49476
Effective search space used:    49476
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 Sep 24 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:

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