GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Thiothrix lacustris DSM 21227

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  229 bits (585), Expect = 7e-65
 Identities = 134/330 (40%), Positives = 195/330 (59%), Gaps = 10/330 (3%)

Query: 4   LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63
           L LS++ K +   EV+   +L I+ GEF   +GPSGCGK+T+LR+IAG E+ + G + ++
Sbjct: 7   LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66

Query: 64  DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123
              +  +   KR    VFQSYAL+PH+TV +N+ F L+ AGV   +I  RV +A  I+ L
Sbjct: 67  GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRL 126

Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183
                RKP QLSGGQ+QRVAI RA+V  PKI L DE LS LD +LR  M++E+ +L +QL
Sbjct: 127 SEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQL 186

Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243
             T VYVTHDQ EA++++D+I+VM  G  +QVG+P ++Y+ P NLFVA FIG  ++N   
Sbjct: 187 GITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG--EINVFD 244

Query: 244 G-VIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDLAIDMLE 302
           G +++   +  Y    +    +I    + A G  V + +RPE         +D   D+ E
Sbjct: 245 GEIVQALGEYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDL------RIDCRPDVAE 298

Query: 303 HLGGETFAYARHHGNGEL-IVVETKNGRGL 331
             G       R +    L   +E +NG+ L
Sbjct: 299 RKGFPGIVLERSYTGQTLNSHIELENGQTL 328


Lambda     K      H
   0.321    0.139    0.396 

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: 340
Number of extensions: 14
Number of successful extensions: 1
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: 358
Length of database: 369
Length adjustment: 29
Effective length of query: 329
Effective length of database: 340
Effective search space:   111860
Effective search space used:   111860
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 (21.8 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