GapMind for catabolism of small carbon sources

 

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

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate H281DRAFT_06397 H281DRAFT_06397 amino acid/amide ABC transporter membrane protein 1, HAAT family

Query= ecocyc::LIVH-MONOMER
         (308 letters)



>FitnessBrowser__Burk376:H281DRAFT_06397
          Length = 286

 Score =  157 bits (397), Expect = 3e-43
 Identities = 100/299 (33%), Positives = 167/299 (55%), Gaps = 22/299 (7%)

Query: 8   FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67
           +L Q+ NG+ +G  Y L+A+G ++V+G++  +NFAHG  YM+G+Y  F   A    M   
Sbjct: 4   YLLQIVNGIGVGMLYFLLAVGLSIVFGLLRFVNFAHGAFYMLGAY--FCYQAMQWSMSFW 61

Query: 68  TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127
           T  ++V        +   A  W +E++  R V   +    ++  +G+++ +Q    L  G
Sbjct: 62  TALIVVP-------IAVGALAWVVEKLILRHVYAQQHEFHILVTVGLALVVQECAILVWG 114

Query: 128 --SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIF--IRYSRMGRA 183
               +VA+P + NG  + G       S    +  ++++ F A+LA  ++  +  +R+G A
Sbjct: 115 PLGDNVAVPDMLNGVVIWG-------SFVYPKYRLFVIGFTAVLAALLWWVLEGTRLGSA 167

Query: 184 CRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAF 243
            RA +E  +M SLLGIN  RV +L F +GAA AA+AGVL     GV +P++G  A   AF
Sbjct: 168 VRAGSESTEMVSLLGINVLRVFSLVFALGAATAALAGVLAAPIRGV-DPFMGIEALGVAF 226

Query: 244 TAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302
              V+GG+G+  GA++GGL++GI +++ S  L  E   ++ +  +  VLL+ P G+LGR
Sbjct: 227 VVVVVGGMGNFLGALVGGLLVGIVQSVMST-LWPEGARLMIYVAMAAVLLLRPNGLLGR 284


Lambda     K      H
   0.328    0.141    0.410 

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: 254
Number of extensions: 17
Number of successful extensions: 5
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: 308
Length of database: 286
Length adjustment: 26
Effective length of query: 282
Effective length of database: 260
Effective search space:    73320
Effective search space used:    73320
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: 48 (23.1 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