GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braE in Azospirillum brasilense Sp245

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS25635 AZOBR_RS25635 high-affinity branched-chain amino acid ABC transporter (permease protein) (fragment)

Query= uniprot:Q1MCU1
         (463 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS25635 AZOBR_RS25635
           high-affinity branched-chain amino acid ABC transporter
           (permease protein) (fragment)
          Length = 328

 Score =  193 bits (491), Expect = 6e-54
 Identities = 125/353 (35%), Positives = 188/353 (53%), Gaps = 35/353 (9%)

Query: 112 LIALLLYPMVVVAIKG-PQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFY 170
           L+ALL++  +   + G  +G    + N     LI+++L+  +++V G+AGLL LG+ AFY
Sbjct: 6   LLALLVFVGLPAVLAGFDRGYFYQIANLA---LIFILLSASMHLVTGVAGLLHLGHAAFY 62

Query: 171 AVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIR 230
            VGAY+ ALLS+ FGL F V LPLSG+ AAL   ++  P +RL   Y A+ TLA G+++ 
Sbjct: 63  GVGAYTAALLSTKFGLGFTVTLPLSGLVAALIAFLVALPTMRLVSIYFAVATLAIGQMLY 122

Query: 231 LVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILAL 290
           LV++NW + TKG  GI       LFG                   + YY +     ++AL
Sbjct: 123 LVMLNWVEFTKGPNGIIVTKGLELFGFSLSGRL------------ATYYTV---ATVVAL 167

Query: 291 CMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFA 350
           C+L      RL     G A  ++RED+    ++G++T   K+ AF   A FAG AGS +A
Sbjct: 168 CVLAIG---RLSHSYYGNALRSIREDDQCADAMGVSTARLKMEAFTLSAFFAGVAGSLWA 224

Query: 351 ARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGP 410
              G++SP  F F ES +ILA+VV+GG+GSL G  I A++++   E LR        FG 
Sbjct: 225 HMTGYISPGDFKFSESILILAMVVVGGLGSLPGAVIGALLLILLPEGLR-------AFGD 277

Query: 411 DFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRERKAISGSFIKEGHG 463
                 +R ++ GL M + +L  P+G +G        R +   +     +G G
Sbjct: 278 ------FRNIMVGLVMFLSILLLPKGLLGEVSALQLARRQLGAAWRNTVKGEG 324


Lambda     K      H
   0.330    0.145    0.432 

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: 436
Number of extensions: 31
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: 463
Length of database: 328
Length adjustment: 30
Effective length of query: 433
Effective length of database: 298
Effective search space:   129034
Effective search space used:   129034
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: 50 (23.9 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