GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Thiothrix lacustris DSM 21227

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

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  239 bits (610), Expect = 9e-68
 Identities = 141/342 (41%), Positives = 203/342 (59%), Gaps = 19/342 (5%)

Query: 4   LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELD 63
           L + N+ K F    ++   +L + D EF   +GPSGCGK+T+LRLIAG E+ + G I L+
Sbjct: 7   LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66

Query: 64  GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILEL 123
           G DI  +   KR    VFQ+YAL+PH++V  N++F L +AGV   ++  +V++A  I+ L
Sbjct: 67  GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRL 126

Query: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKEL 183
                RKP QLSGGQ+QRVAI RA+V  PKI L DE LS LD  LR QM+LEL +L ++L
Sbjct: 127 SEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQL 186

Query: 184 QATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLK 243
             T +YVTHDQ EA++M+D+++V++ G+ +QVG+P ++Y  P NLFVA F+G  ++    
Sbjct: 187 GITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG--EINVFD 244

Query: 244 GKITRVDSQGCEVQLDAGTR--VSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQVT 301
           G+I  V + G E Q +A     V         +VG  V + +RPE L +    DC     
Sbjct: 245 GEI--VQALG-EYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDLRI----DC----R 293

Query: 302 ADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLH 343
            DV+ER G       R+ +G+ L   +        G+TL  H
Sbjct: 294 PDVAERKGFPGIVLERSYTGQTLNSHIE----LENGQTLMAH 331


Lambda     K      H
   0.320    0.137    0.389 

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: 320
Number of extensions: 11
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: 367
Length of database: 369
Length adjustment: 30
Effective length of query: 337
Effective length of database: 339
Effective search space:   114243
Effective search space used:   114243
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