GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlA in Klebsiella michiganensis M5al

Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate BWI76_RS27160 BWI76_RS27160 PTS mannitol transporter subunit IICBA

Query= BRENDA::P00550
         (637 letters)



>FitnessBrowser__Koxy:BWI76_RS27160
          Length = 636

 Score = 1164 bits (3011), Expect = 0.0
 Identities = 598/636 (94%), Positives = 612/636 (96%), Gaps = 1/636 (0%)

Query: 1   MSSDIKIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLL 60
           MSSDIKIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLL
Sbjct: 1   MSSDIKIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLL 60

Query: 61  PLLIGYTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDG 120
           PLLIGYTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGW IK FD WVDG
Sbjct: 61  PLLIGYTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWAIKKFDVWVDG 120

Query: 121 KIKSGFEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIF 180
           KIKSGFEMLVNNFSAGIIGMILAILAFLGIGP VE LSK+LAAGVNFMV H+MLPLASIF
Sbjct: 121 KIKSGFEMLVNNFSAGIIGMILAILAFLGIGPAVEILSKILAAGVNFMVAHEMLPLASIF 180

Query: 181 VEPAKILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAK 240
           VEPAKILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAK
Sbjct: 181 VEPAKILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAK 240

Query: 241 QSAGGAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSI 300
           QSAGGAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTIL GGLVSPASPGSI
Sbjct: 241 QSAGGAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILNGGLVSPASPGSI 300

Query: 301 LAVLAMTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKAESK 360
           LAVLAMTPKGAYFANIA + AAMAVSFVV+A+LLKTSKVKEEDDIEAATRRM DMKAESK
Sbjct: 301 LAVLAMTPKGAYFANIAAIVAAMAVSFVVAAVLLKTSKVKEEDDIEAATRRMHDMKAESK 360

Query: 361 -GASPLSAGDVTNDLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAINN 419
            GA+PL+AGDV NDLSHVRKIIVACDAGMGSSAMGAGVLRKK+QDAGLS ISVTN AINN
Sbjct: 361 GGATPLAAGDVANDLSHVRKIIVACDAGMGSSAMGAGVLRKKVQDAGLSNISVTNCAINN 420

Query: 420 LPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQRHTANEEKVK 479
           LPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQRHT NEEKV+
Sbjct: 421 LPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQRHTDNEEKVR 480

Query: 480 DSLKDSFDDSSANLFKLGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDRE 539
           DSLKDSFD +  NLFKLGAENIFLGRKAATKEEAI FAGEQLVKGGYVEPEYVQAMLDRE
Sbjct: 481 DSLKDSFDAADTNLFKLGAENIFLGRKAATKEEAILFAGEQLVKGGYVEPEYVQAMLDRE 540

Query: 540 KLTPTYLGESIAVPHGTVEAKDRVLKTGVVFCQYPEGVRFGEEEDDIARLVIGIAARNNE 599
           KLT TYLGESIAVPHGT+EAKDRVLKTG+VFCQYPEGVRFGEEED++ARLVIGIAARNNE
Sbjct: 541 KLTSTYLGESIAVPHGTIEAKDRVLKTGIVFCQYPEGVRFGEEEDEVARLVIGIAARNNE 600

Query: 600 HIQVITSLTNALDDESVIERLAHTTSVDEVLELLAG 635
           HIQVITSLTNALDDESVIERL  TTSVDEVL LL G
Sbjct: 601 HIQVITSLTNALDDESVIERLTKTTSVDEVLTLLKG 636


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: 1348
Number of extensions: 40
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: 637
Length of database: 636
Length adjustment: 38
Effective length of query: 599
Effective length of database: 598
Effective search space:   358202
Effective search space used:   358202
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 17 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