GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS25635
          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 (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