GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlA in Megamonas funiformis YIT 11815

Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_008540051.1 HMPREF9454_RS11685 PTS mannitol transporter subunit IICBA

Query= BRENDA::P00550
         (637 letters)



>NCBI__GCF_000245775.1:WP_008540051.1
          Length = 631

 Score =  671 bits (1730), Expect = 0.0
 Identities = 343/606 (56%), Positives = 441/606 (72%), Gaps = 14/606 (2%)

Query: 8   KVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLIGYT 67
           K+Q FGRFLS MVMPNIGAFIAWG++TALFIPTGW+PNE LA   GPM  +L+PLLIGY+
Sbjct: 13  KMQKFGRFLSGMVMPNIGAFIAWGLLTALFIPTGWIPNEYLAAAGGPMSKWLIPLLIGYS 72

Query: 68  GGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKSGFE 127
           GG  +   RGGV+GAI T G+I G+D+PMFLG+MI GP GGWCIK FD     KI +GFE
Sbjct: 73  GGSAIYQHRGGVLGAIATAGIIAGSDIPMFLGAMIVGPFGGWCIKKFDEAFQDKIPTGFE 132

Query: 128 MLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPAKIL 187
           ML+NNFSAGI+G ILAILA+  +GP+V +L+ +L  GV F+V   ++PL SI VEPAK+L
Sbjct: 133 MLINNFSAGILGGILAILAYAIVGPVVSSLNDILRGGVEFIVNLGLIPLVSILVEPAKVL 192

Query: 188 FLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAGGAA 247
           FLNNAINHG+FSP+GIQ+S ELGKSIFF+IE+NPGPG+GVLLA+   G+G AK SA GA 
Sbjct: 193 FLNNAINHGVFSPIGIQESQELGKSIFFMIESNPGPGLGVLLAFCLVGKGMAKSSAPGAV 252

Query: 248 IIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVLAMT 307
           IIHFLGGIHEIYFPY+LM P L+LAVI  GM GVFTL++L GGL++PASPGSI A+LAMT
Sbjct: 253 IIHFLGGIHEIYFPYILMKPILLLAVIPAGMAGVFTLSVLNGGLIAPASPGSIFAILAMT 312

Query: 308 PKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKAESKGASPLSA 367
           PKGAYFANIA V  A AVSFV+++I +K SK  +   +E A + MQDMK  ++G+  + +
Sbjct: 313 PKGAYFANIAAVVVATAVSFVIASIFIKASK-DDGSSLEEAQQNMQDMK--NRGSKRVES 369

Query: 368 GDVTNDLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAINNLPPDVDLV 427
            DV    S ++KII ACDAGMGSSAMGA  LR K++ AG   ISVTN AI N+P D  +V
Sbjct: 370 -DVVVKGSELKKIIYACDAGMGSSAMGASALRNKLKKAGYGYISVTNCAIGNIPSDAQIV 428

Query: 428 ITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQRHTANEEKVKDSLKDSFD 487
           ++H  L +RA+   PQA+H+ + +F+ + +Y  +  +L   Q   A  E+V DS +++ +
Sbjct: 429 VSHEKLADRAIADSPQAEHLFVQDFIKNDVYDIILAKL---QNVEAKVEEVTDSKENAVE 485

Query: 488 DSSANLFKLGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLTPTYLG 547
           D +     L  ENI +     TKEEAI+ AGE L K GYV  EY+  ML RE+   TY+G
Sbjct: 486 DETV----LKRENIKMCLDTVTKEEAIKMAGELLYKSGYVGKEYINGMLAREQDVSTYMG 541

Query: 548 ESIAVPHGTVEAKDRVLKTGVVFCQYPEGVRFGEEEDDIARLVIGIAARNNEHIQVITSL 607
             IA+PHG    KD V K+G+V  Q+P GV FG  +   A+LV+GIA + +EH+ ++ ++
Sbjct: 542 RGIAIPHGENAVKDTVKKSGIVVLQFPNGVEFGTGK---AKLVVGIAGKGDEHLAILANI 598

Query: 608 TNALDD 613
             ALD+
Sbjct: 599 AIALDE 604


Lambda     K      H
   0.321    0.138    0.397 

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: 1029
Number of extensions: 49
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 637
Length of database: 631
Length adjustment: 38
Effective length of query: 599
Effective length of database: 593
Effective search space:   355207
Effective search space used:   355207
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: 54 (25.4 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