GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Desulfatiglans anilini DSM 4660

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_028320915.1 H567_RS0107410 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_000422285.1:WP_028320915.1
          Length = 291

 Score =  150 bits (380), Expect = 3e-41
 Identities = 101/299 (33%), Positives = 160/299 (53%), Gaps = 24/299 (8%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M+ F+Q L+ G+  G +YGL+ +G +++ G++G+IN AHG + M+  +   + F  L   
Sbjct: 1   MDVFLQTLVAGILKGGLYGLIGMGMSLIMGVMGIINLAHGQLMMVAMYITFVCFTYL--- 57

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAP---LITAIGMSITLSN 117
             GL     LL+ +    L+ +L    I+R A  PL     L P   ++  +G+ + L+ 
Sbjct: 58  --GLDPYAALLITMPALFLLGAL----IQRYALNPLMEVESLLPENQVLMTVGIGMVLTE 111

Query: 118 FIQVTQGPRNKPIPPMVSSVYQFG---NISVSLKQIIIIVITAVLLT--IFWYIVNRTAL 172
             +       K +    SS   F    + SV+L     I   A+L T  +FW+++ +T L
Sbjct: 112 IARFIFSSDYKSVQTAYSSSSFFLRGISFSVALTAAFFI---ALLFTGFMFWFLL-KTDL 167

Query: 173 GRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYL-MYYGVASFNDGFTPG 231
           GRA RAT QD+  A L+GV+  +   +TF +G+AL A AGT+ + +YY        FT  
Sbjct: 168 GRAIRATAQDKDAALLMGVDAKRITILTFGIGSALVAAAGTLLMPIYYLFPDIGSPFTR- 226

Query: 232 VKAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTG 290
            KAF   +LGG+GS  GA+FGGL +GL E+  + Y  +A+ D+    I   VL+F P+G
Sbjct: 227 -KAFVITILGGLGSTVGAIFGGLTLGLAEAFGATYIGMAFDDMIGLLIFILVLLFLPSG 284


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: 285
Number of extensions: 22
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: 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 Apr 09 2024. 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