Alignments for a candidate for mtlA in Klebsiella michiganensis M5al

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources