GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Azospirillum thiophilum BV-S

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_045585061.1 AL072_RS29560 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_001305595.1:WP_045585061.1
          Length = 301

 Score =  379 bits (974), Expect = e-110
 Identities = 194/303 (64%), Positives = 243/303 (80%), Gaps = 5/303 (1%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           M+YF+QQL+NGL+LG+IYGL+AIGYTMVYGIIGMINFAHG+I+M+G F ALI FL + ++
Sbjct: 1   MDYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGAL 60

Query: 61  -FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFI 119
               +P+A  LL+MLV +ML TS++ WT+ER+AYRPLR S RLAPLI+AIGMSI L N+I
Sbjct: 61  GITWVPLA--LLIMLVASMLFTSVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYI 118

Query: 120 QVTQGPRNKPIPPMVSS--VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQR 177
           Q+ QG R+KP+ P++        G +SVS  ++  IVIT VL+  F  ++NRT+LGRAQR
Sbjct: 119 QILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITLVLMVGFTILINRTSLGRAQR 178

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

Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297
           AVLGG+GSLPGA+ GG++IGLIE+ WS Y    +KDVATF+IL  VLIF+PTG+LGRPE+
Sbjct: 239 AVLGGVGSLPGAMLGGVVIGLIEAFWSGYVGSEWKDVATFSILVLVLIFRPTGLLGRPEI 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: 418
Number of extensions: 17
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 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