GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Amycolatopsis halophila YIM 93223

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_034268201.1 AMYHA_RS04370 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_000504245.1:WP_034268201.1
          Length = 291

 Score =  144 bits (362), Expect = 3e-39
 Identities = 90/298 (30%), Positives = 161/298 (54%), Gaps = 13/298 (4%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M   +QQL NGL  GS Y L+A+G ++++G++G++NFAHG  +MLG F A   F++L S 
Sbjct: 1   MSGLLQQLFNGLVSGSFYALLALGLSVIFGMLGVVNFAHGAFYMLGAFGA---FVLLDS- 56

Query: 61  FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120
            AGL      L +LVV +L+  +    +ER+    L   F L   +   G+++ L + I+
Sbjct: 57  -AGLS---WWLALLVVPILL-GVIGMVLERLFVHRLMHLFPLYNFLLTFGIALILQDLIR 111

Query: 121 VTQGPRNKPI--PPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRA 178
           +  G  ++P   P ++      G  +    Q+ + V +  L  + W +++RT +G   RA
Sbjct: 112 MKYGVTSQPYARPSILDGSVDLGLFTYPKYQVFVFVFSIALSGLVWLVLSRTRVGMIVRA 171

Query: 179 TEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAA 238
           + +  ++   LG++V + ++  F  G ALA +AG +      V S + G    +  F   
Sbjct: 172 STERAELTQSLGIDVRRWVTPVFGFGIALAGLAGVLAAPMRAVNS-SMGADLIIVIFAVV 230

Query: 239 VLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPE 296
           V+GG+GS+ G+V  G ++G++ ++ + ++  A      F ++A VL+ +P G+ GR E
Sbjct: 231 VIGGLGSVLGSVAAGYIVGMVTAIGN-FYVPALSQSLVFVLMALVLLLRPAGLFGREE 287


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: 292
Number of extensions: 18
Number of successful extensions: 5
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 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