GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC26dg in Paraburkholderia bryophila 376MFSha3.1

Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate H281DRAFT_01715 H281DRAFT_01715 sulfate permease, SulP family

Query= TCDB::Q1J2S8
         (499 letters)



>FitnessBrowser__Burk376:H281DRAFT_01715
          Length = 553

 Score =  243 bits (619), Expect = 2e-68
 Identities = 158/511 (30%), Positives = 257/511 (50%), Gaps = 52/511 (10%)

Query: 22  RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81
           R D+  G+   +  +P A+AF + +G+ P  GLY + +  ++ A  GG P  I+  TG M
Sbjct: 18  RGDIFGGVAAGVVALPLALAFGVASGLGPVAGLYGAIVTGIVAALFGGTPVQITGPTGPM 77

Query: 82  ALLMTGLVKDH-------GIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNA 134
            L++ G++  +        +  +    V+ G +Q+ FG  ++  Y+++VP  V+ GF++ 
Sbjct: 78  TLVVAGVLAANMHSSGSANLPLVVGIFVVAGFMQIAFGLLRIGSYIRYVPYPVISGFMSG 137

Query: 135 LAILIFMAQLPQFVGAN---------------------WQMYAMVAAGLAIIYLLPLVFK 173
           + ++I   Q+    GAN                     W   A+ A+ +AI  LLP   K
Sbjct: 138 IGVIIITQQVFPMFGANAPGSDPWSILSQLHLLGGNIKWSAVALSASTIAIALLLPRFTK 197

Query: 174 AMPSALVAIVVLTVVAVVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALT 233
            +P++LVA++VLT+ AV+   DV  +G+   +P+ LP    P   L    L  + P AL 
Sbjct: 198 VIPASLVALIVLTITAVMLKLDVPVIGE---IPSGLPTLTMPAFDL--HRLPSLVPAALQ 252

Query: 234 LSLVGLLESLLTAQLIDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVT 293
           LSL+G ++SLLTA + D  T T  D N E  GQG+ NI     GG+ G     ++++NV 
Sbjct: 253 LSLLGAIDSLLTALVADNLTRTRHDSNRELIGQGLGNIAAAVIGGLPGAGATMRTVVNVD 312

Query: 294 SGGRGRLSTFVAGAFLMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPK 353
           +GGR RLS  + G FL  ++L L  LL  +P A L  +++ V I   D  S R L    +
Sbjct: 313 AGGRTRLSGVIHGLFLAAVLLGLSGLLQHVPRAILAGLLVTVGIGIIDRRSFRHLLKLSR 372

Query: 354 GETVVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQLSQ----VTPV------DEV 403
            +  +ML  +A+TVFT DL + V  G+V+++  F +KV  +++    +TPV      DE+
Sbjct: 373 SDAFLMLLVLALTVFT-DLIIAVATGLVVASFVFVKKVGDITEQRTMLTPVADEPWADEL 431

Query: 404 -------DGTRTYRVRGQLFFVSTHDFLH-QFDFTHPARRVVIDLSDAHFWDGSAVGALD 455
                  D      V G +FF     FL      T  +R +V+ +    + D + V ALD
Sbjct: 432 TIPAGLRDRLLIKHVDGPIFFGFASKFLDIARQATLLSRLLVLRMDRISYMDQTGVYALD 491

Query: 456 KVMLKFMRQGTSVELRGLNAASATLVERLAV 486
             +++    G  V + G++ +   L+ERL V
Sbjct: 492 DALVRLNAAGVRVLVVGVSVSQRDLLERLQV 522


Lambda     K      H
   0.328    0.140    0.407 

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: 546
Number of extensions: 34
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 499
Length of database: 553
Length adjustment: 35
Effective length of query: 464
Effective length of database: 518
Effective search space:   240352
Effective search space used:   240352
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: 52 (24.6 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