GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Pseudomonas fluorescens FW300-N2E2

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate Pf6N2E2_1800 putative ABC transporter ATP-binding protein

Query= TCDB::P0AAG3
         (241 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1800
          Length = 254

 Score =  240 bits (612), Expect = 2e-68
 Identities = 122/244 (50%), Positives = 170/244 (69%), Gaps = 10/244 (4%)

Query: 6   NVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDGIVV 65
           +++K+Y  F  L D + EV++GEV+ + GPSGSGKSTL++ VN LE + +G + VDG +V
Sbjct: 9   SLNKYYDQFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGLWVDGELV 68

Query: 66  NDK----------KTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPARE 115
             +          +T +A+ R   GMVFQ F LFPH+++++N+     +VLKR    A E
Sbjct: 69  GYRIVGNKLHELNETQIARQRLSTGMVFQRFNLFPHMTVLQNIIEGPCQVLKRSPKEANE 128

Query: 116 KALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEV 175
           +AL+LL RVGL+   N +P +LSGGQQQRVAIARAL M P  MLFDEPTSALDPE++ EV
Sbjct: 129 EALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALDPELVGEV 188

Query: 176 LDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDF 235
           L VM +LA  GMTM+VVTHE+GFAR+V+NR++FMD G+IVE    +     P++ R + F
Sbjct: 189 LSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDGGQIVEAGSPEEILISPQNPRTQSF 248

Query: 236 LAKI 239
           ++ +
Sbjct: 249 ISAV 252


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: 175
Number of extensions: 6
Number of successful extensions: 2
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: 254
Length adjustment: 24
Effective length of query: 217
Effective length of database: 230
Effective search space:    49910
Effective search space used:    49910
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 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:

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