GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcaP in Lysobacter daejeonensis GH1-9

Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_036136365.1 N800_RS06840 amino acid permease

Query= TCDB::S6EX81
         (469 letters)



>NCBI__GCF_000768355.1:WP_036136365.1
          Length = 474

 Score =  232 bits (591), Expect = 2e-65
 Identities = 141/441 (31%), Positives = 225/441 (51%), Gaps = 9/441 (2%)

Query: 30  ALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMSTVMPFAGSAY 89
           ALG+G +I   IF + GQ AA  AGP ++ S++LAA+   F ALAYAE ++++P +GSAY
Sbjct: 34  ALGIGAVIGGGIFVITGQAAADHAGPAIMLSFVLAAICCTFCALAYAEFASMVPVSGSAY 93

Query: 90  SWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPKVLA-----N 144
           ++     GE   W  GW L+ EY ++ + V   ++     LL     HLP  L      +
Sbjct: 94  TYTYATLGELAAWFIGWMLVLEYGVSASAVAVSWTGYFLSLLEHFNIHLPAALVQAPLDS 153

Query: 145 PFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVGITVIKPA 204
                G + ++ +  ++LL   + + G   +  ++  +V+LK   ++  II G   + PA
Sbjct: 154 KLQPTGAIANLPAAAIVLLLTWVCYIGIRKSSGMNTAMVLLKSGLIVLVIIAGWQYVDPA 213

Query: 205 NYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSL 264
           N+ PFIP  N   G  G+ G+  G SM+F AYIGF++++  + E+ NPQK +P G++ SL
Sbjct: 214 NWEPFIPA-NEGPGKFGWEGVLRGASMVFFAYIGFEAVSVAAQESHNPQKDLPFGMLMSL 272

Query: 265 LIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTAIALAGMFIALLG 324
            I  VL+  +  V+ G+ PY+    +   V      +  + L  VV   AL G+   +L 
Sbjct: 273 AICTVLYIGMAAVMTGLTPYTLLGTDEPVVTAVAGHAELAWLRVVVEIGALIGLSSVVLV 332

Query: 325 MVLAGSRLLYAFGRDGLLPKGLGKMNARN-LPANGVWTLAIVAIVIGAFFPFAFLAQLIS 383
           M++   R+     RDGLLP+   +++ ++  P        I   ++ A FP   L +L S
Sbjct: 333 MIIGQPRIFMIMARDGLLPEVFTRIHPKHRTPHINTVITGIGIALLAAVFPLDILGELTS 392

Query: 384 AGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLY 443
            GTLIAF  V  G+  LRR Q  DLP   +++     +   G    L +   + +   + 
Sbjct: 393 MGTLIAFGAVCAGVLILRRTQ-PDLPR-PFRIRGVWFVCLAGIFSCLALLSAMTLHNWML 450

Query: 444 SGIWFLIGILIYFAYGNRRSR 464
              W  +G  IYF YG R S+
Sbjct: 451 MLGWTTVGFAIYFLYGYRHSK 471


Lambda     K      H
   0.328    0.143    0.433 

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: 607
Number of extensions: 35
Number of successful extensions: 6
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: 469
Length of database: 474
Length adjustment: 33
Effective length of query: 436
Effective length of database: 441
Effective search space:   192276
Effective search space used:   192276
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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