GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Paraburkholderia bryophila 376MFSha3.1

Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate H281DRAFT_03349 H281DRAFT_03349 amino acid ABC transporter membrane protein, PAAT family

Query= SwissProt::P0AER3
         (246 letters)



>FitnessBrowser__Burk376:H281DRAFT_03349
          Length = 222

 Score =  120 bits (300), Expect = 3e-32
 Identities = 76/222 (34%), Positives = 121/222 (54%), Gaps = 16/222 (7%)

Query: 23  GW--IWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNR-FLSGLGTLYVELFRNVPLIV 79
           GW  I  G  VT+ ++  +  ++ ++G   GI R  P R  + G  T Y+  FR  PL+V
Sbjct: 11  GWPDIMHGAIVTVEVTAASLALSCVLGLLIGIGRLTPQRRIVYGFCTAYLTFFRGTPLLV 70

Query: 80  QFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLGLFTAARVCEQVRAAIQSLPR 139
           Q F  +  +P+      G+   A        FL  ML LGL++AA V E VR AIQS+ R
Sbjct: 71  QLFLLFFGLPQF-----GILLPA--------FLCGMLGLGLYSAAYVSEIVRGAIQSVDR 117

Query: 140 GQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSAIASTIGLVDMAAQAG 199
           GQ  AA ++G++  QA R ++LP A   ++PP+ +E + L+KNSA+ S + + D+  +  
Sbjct: 118 GQMEAARSIGMSSGQAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQ 177

Query: 200 KLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRLPG 241
           K++  S  + E + AI L Y+++       +  VER++R  G
Sbjct: 178 KIISVSYRSLEVYLAIALVYLVLTQATNYALHRVERRLRAGG 219


Lambda     K      H
   0.328    0.140    0.443 

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: 152
Number of extensions: 9
Number of successful extensions: 3
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: 246
Length of database: 222
Length adjustment: 23
Effective length of query: 223
Effective length of database: 199
Effective search space:    44377
Effective search space used:    44377
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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