GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Thiothrix lacustris DSM 21227

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= CharProtDB::CH_001555
         (400 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  192 bits (487), Expect = 2e-53
 Identities = 98/227 (43%), Positives = 148/227 (65%), Gaps = 6/227 (2%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           + D +L I++GE F I+G SG GK+T++RL+    +P  GQ+L++G DIA+I        
Sbjct: 22  LSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGDDIARIP------A 75

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPD 163
            ++    VFQS+AL PH+TV DN AFG+++AG++ ++   +  DAL  V L  +A   P 
Sbjct: 76  EKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSEFATRKPH 135

Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223
           +LSGG +QRV +ARA+   P ILL+DE+ SALD  +R +MQ EL +LQ +   T V+++H
Sbjct: 136 QLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGITFVYVTH 195

Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDI 270
           D +EA+ + DRI +M NG+  QVGTP EI  +P N +V  F   +++
Sbjct: 196 DQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGEINV 242


Lambda     K      H
   0.319    0.137    0.378 

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: 363
Number of extensions: 16
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: 400
Length of database: 369
Length adjustment: 30
Effective length of query: 370
Effective length of database: 339
Effective search space:   125430
Effective search space used:   125430
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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