GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06397 H281DRAFT_06397 amino
           acid/amide ABC transporter membrane protein 1, HAAT
           family
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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