GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Azospirillum brasilense Sp245

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS08235 AZOBR_RS08235 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__azobra:AZOBR_RS08235
          Length = 301

 Score =  377 bits (969), Expect = e-109
 Identities = 195/303 (64%), Positives = 240/303 (79%), Gaps = 5/303 (1%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           MEYF+QQL+NGL+LG+IYGL+AIGYTMVYGIIGMINFAHG+I+M+G F ALI FL + S+
Sbjct: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60

Query: 61  -FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFI 119
               +P+A  LLVMLV +ML T+++ WT+ER+AYRPLR S RLAPLI+AIGMSI L N++
Sbjct: 61  GITWVPLA--LLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYV 118

Query: 120 QVTQGPRNKPIPPMVSS--VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQR 177
           Q+ QG R+KP+ P++        G +SVS  ++  IVIT  L+  F  ++ RT+LGRAQR
Sbjct: 119 QILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQR 178

Query: 178 ATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTA 237
           A EQD+KMA LLGVNVD+ IS+TFVMGAALAAVAG M L+ YGV  F  GF  GVKAFTA
Sbjct: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTA 238

Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297
           AVLGGIGSLPGA+ GG++IGLIE+ WS Y    +KDVATF IL  VLIF+PTG+LGRPE+
Sbjct: 239 AVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEI 298

Query: 298 EKV 300
           EKV
Sbjct: 299 EKV 301


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: 419
Number of extensions: 18
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: 301
Length adjustment: 27
Effective length of query: 273
Effective length of database: 274
Effective search space:    74802
Effective search space used:    74802
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