GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Methanospirillum lacunae Ki8-1

Align KguT (characterized, see rationale)
to candidate WP_109968169.1 DK846_RS06735 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>NCBI__GCF_003173355.1:WP_109968169.1
          Length = 425

 Score =  178 bits (452), Expect = 2e-49
 Identities = 126/415 (30%), Positives = 207/415 (49%), Gaps = 36/415 (8%)

Query: 13  YIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIY 72
           +I+P   + Y +A+LDR N G+AA   M  DL I+  L   +  +FF+GY  F+VP  I 
Sbjct: 18  HIIPFALLLYIVAFLDRVNLGYAAIV-MNPDLGISAELFGFISGIFFIGYLIFEVPSNII 76

Query: 73  AEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFT 132
            +K   +  I   +I WG +A L G VQS   LI +RFLLG+ EA   P M+ YL  WF 
Sbjct: 77  MQKVGARIWIGRIMISWGLVAVLMGFVQSPEHLIILRFLLGIAEAGFFPGMIWYLGTWFP 136

Query: 133 RAERSRA----NTFLILGNPV----------TILWMSVVSGYLVKHFDWRWMFIIEGLPA 178
               +R+    +T +++ N +          T+ W SV S        WRW+FIIEG+PA
Sbjct: 137 HRYLARSIALFSTAIVISNIIGAPLSMYILDTVNWGSVAS--------WRWLFIIEGIPA 188

Query: 179 VLWAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYR--EAFRSPKVIIL 236
           +L+  +   ++ +RP  A WL + +K  L   L   + G   +K++R  +     +V++ 
Sbjct: 189 ILFGVLSLFILKNRPADAGWLDSDQKQWLVSEL---ESGTIRMKSHRLGDILTDTRVLLF 245

Query: 237 SLQYFCWSIGVYGFVLWLPSILKQ-AAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQ 295
           S  YF  ++G+Y  + +LP++       LD+   G +  +PY+  ++ M  VS  SD   
Sbjct: 246 SGTYFAVTVGMYAIIFFLPTLSSSFLHDLDMRVIGLILMIPYIVTLICMFLVSSHSDLRG 305

Query: 296 KRKRFVWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSN 355
           +R   +     IA        +   E    S   + IA + + +  GPF++ V  +   +
Sbjct: 306 ERLYHIIILFFIAGAGLTLDQL--AEDPILSLLGITIALSGILSIIGPFWSYVLSVFTPD 363

Query: 356 VAGGAMALINSMGALGSFSGSWLVGYLNGV-----TGGPGASYLFMCGALLVAVA 405
                +A+INS+G LG F G  + GYL  +     +G P  +++   GA+++ +A
Sbjct: 364 EQPVGVAVINSIGNLGGFVGPVITGYLISLFKTLDSGWPVITFILCLGAVMIFMA 418


Lambda     K      H
   0.328    0.140    0.457 

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: 568
Number of extensions: 33
Number of successful extensions: 6
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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: 51 (24.3 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