GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Thiothrix lacustris DSM 21227

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  186 bits (473), Expect = 7e-52
 Identities = 103/255 (40%), Positives = 159/255 (62%), Gaps = 6/255 (2%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           MT   +  LS I K+  ++ + + + ++TI  G  F +LGPSG GKTT LRLIAG E+P 
Sbjct: 1   MTRSPILTLSNISKRFASQ-EVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPN 59

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I  + + ++      +  EKR    VFQ++AL+P++TVFDN+AF LK+A V    I 
Sbjct: 60  EGQILLNGDDIAR-----IPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIA 114

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +V +    + LS    R P +LSGGQ QR AIARA+V  PK+LLLDE  S LD ++R+ 
Sbjct: 115 VRVADALAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQ 174

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            +  ++++QR+  +T + V+HD  +  +++++  V+ NG+  Q+GTP EIYE P    +A
Sbjct: 175 MQLELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVA 234

Query: 241 RLTGEINLIQAKIIE 255
           +  GEIN+   +I++
Sbjct: 235 QFIGEINVFDGEIVQ 249


Lambda     K      H
   0.317    0.136    0.374 

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: 284
Number of extensions: 15
Number of successful extensions: 2
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: 371
Length of database: 369
Length adjustment: 30
Effective length of query: 341
Effective length of database: 339
Effective search space:   115599
Effective search space used:   115599
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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