GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Haloterrigena daqingensis JX313

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_076583323.1 BB347_RS14205 phosphonate ABC transporter ATP-binding protein

Query= TCDB::P0AAG3
         (241 letters)



>NCBI__GCF_001971705.1:WP_076583323.1
          Length = 280

 Score =  151 bits (381), Expect = 2e-41
 Identities = 95/241 (39%), Positives = 142/241 (58%), Gaps = 11/241 (4%)

Query: 1   MITLKNVSKWY-GHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEIT 59
           M+T +N+SK Y G  + L   S +V   EVV + GPSG+GKSTLI+ +N L     GEI 
Sbjct: 1   MLTAQNISKTYPGGEEALRGVSFDVTGDEVVAIIGPSGAGKSTLIECINRLTEPTDGEIR 60

Query: 60  VDGIVVND-KKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLK-----RDKAPA 113
           +D + V       L + R  + M+FQ + L   L+++EN+   ++  L      R K PA
Sbjct: 61  LDDVTVTALSDRQLRRTRRDIAMIFQEYNLVERLTVMENVLSGRLGYLSTWNAFRRKFPA 120

Query: 114 R--EKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEM 171
              E A + LERVGL  H      +LSGGQ+QRV IARA+   P  ML DEPTS+LDPE 
Sbjct: 121 EDIEFARETLERVGLGGHERDRADELSGGQRQRVGIARAVVQRPKIMLADEPTSSLDPET 180

Query: 172 INEVLDVMVEL-ANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSD 230
            + V++++ E+ A+E + +++  HE+  A + A+R+I + +G++V D P +A  D+   D
Sbjct: 181 SHAVMELLTEIAADERIPVLINIHEVELAVEYADRIIGLADGELVFDGPPEA-LDETAKD 239

Query: 231 R 231
           R
Sbjct: 240 R 240


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: 169
Number of extensions: 15
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: 280
Length adjustment: 24
Effective length of query: 217
Effective length of database: 256
Effective search space:    55552
Effective search space used:    55552
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 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