GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Phaeobacter inhibens BS107

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF247 PGA1_c02590 putative high-affinity branched-chain amino acid transport system permease protein LivH

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Phaeo:GFF247
          Length = 291

 Score =  149 bits (377), Expect = 6e-41
 Identities = 98/297 (32%), Positives = 154/297 (51%), Gaps = 10/297 (3%)

Query: 5   VQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGL 64
           VQ L++GL  G +YGL+A+G+ ++Y     +NFA GD  MLG F    V L LT+    L
Sbjct: 4   VQLLVSGLANGCVYGLIALGFVLIYKATEAVNFAQGDFMMLGAF----VTLGLTNA-EYL 58

Query: 65  PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQG 124
            +   L   L +A +M  L  + ++ V  R L G  + A +I  I +   +  F     G
Sbjct: 59  HLPFWLAAPLSIA-IMAGL-GYLLDLVILRHLFGQNQTAVVILTIALGFVIRFFAGAIWG 116

Query: 125 PRNKPIP-PMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDR 183
              + +  P+     Q   + + L  + II++T +L    +    RT LG A +A  Q++
Sbjct: 117 HEPQTLESPLALGDVQLAGVVLGLADLAIIIVTVLLTWSLYQFFQRTKLGLAMQAASQNQ 176

Query: 184 KMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGGI 243
             A  +G+ V +   + + +  A AAVAG ++    G    N G   G+KAF AAV+GG 
Sbjct: 177 MAAYFMGIPVKRVQGLIWGLSGATAAVAGILFASK-GAIDPNAGLL-GIKAFAAAVIGGF 234

Query: 244 GSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300
           GSLPGA+ GGL++G+IE   + Y    Y  +A + +L  VL+F+P G+  +   +KV
Sbjct: 235 GSLPGALAGGLIVGVIEPFAARYLAAGYSQIAPYVLLLAVLVFRPHGLFSQVRTKKV 291


Lambda     K      H
   0.329    0.143    0.421 

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: 277
Number of extensions: 16
Number of successful extensions: 3
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: 300
Length of database: 291
Length adjustment: 26
Effective length of query: 274
Effective length of database: 265
Effective search space:    72610
Effective search space used:    72610
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 (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