Alignments for a candidate for cmtA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for cmtA in Klebsiella michiganensis M5al

Align PTS system, mannitol-specific IICBA component aka EIICBA-Mtl aka Mannitol-permease IIABC component aka Phosphotransferase enzyme II, CBA component aka EC 2.7.1.69 aka EII-Mtl, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF (characterized)
to candidate BWI76_RS27160 BWI76_RS27160 PTS mannitol transporter subunit IICBA

Query= TCDB::P42956
         (478 letters)



>FitnessBrowser__Koxy:BWI76_RS27160
          Length = 636

 Score =  585 bits (1509), Expect = e-171
 Identities = 298/468 (63%), Positives = 363/468 (77%), Gaps = 8/468 (1%)

Query: 11  MKVKVQRFGSYLSGMIMPNIGAFIAWGIITALFIPAGWFPNEQLNTLVSPMITYLLPLLI 70
           +K+KVQ FG +LS M+MPNIGAFIAWGIITALFIP GW PNE L  LV PMITYLLPLLI
Sbjct: 5   IKIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLI 64

Query: 71  AYTGGKMIYDHRGGVVGATAAIGVIVGSDIPMFLGAMIMGPLGGYLIKQTDKLFKDKVKQ 130
            YTGGK++   RGGVVGA   +GVIVG+D+PMFLG+MI GPLGG+ IK+ D     K+K 
Sbjct: 65  GYTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWAIKKFDVWVDGKIKS 124

Query: 131 GFEMLINNFTAGIVGAALTILAFYAIGPVVLTLNKLLAAGVEVIVHANLLPVASVFVEPA 190
           GFEML+NNF+AGI+G  L ILAF  IGP V  L+K+LAAGV  +V   +LP+AS+FVEPA
Sbjct: 125 GFEMLVNNFSAGIIGMILAILAFLGIGPAVEILSKILAAGVNFMVAHEMLPLASIFVEPA 184

Query: 191 KVLFLNNAINHGILSPIGIEQASQTGKSILFLVEANPGPGLGILLAYMFFGKGSSKSTAP 250
           K+LFLNNAINHGI SP+GI+Q+ + GKSI FL+EANPGPG+G+LLAYMFFG+GS+K +A 
Sbjct: 185 KILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAG 244

Query: 251 GAAIIHFFGGIHEIYFPYILMKPALILAAIAGGASGLLTFTIFNAGLVAAASPGSIIALM 310
           GAAIIHF GGIHEIYFPY+LM P LILA I GG +G+ T TI N GLV+ ASPGSI+A++
Sbjct: 245 GAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILNGGLVSPASPGSILAVL 304

Query: 311 AMTPRGGYFGVLAGVLVAAAVSFIVSAVILKSSKASEE-DLAAATEKMQSMKGKKSQAAA 369
           AMTP+G YF  +A ++ A AVSF+V+AV+LK+SK  EE D+ AAT +M  MK +    A 
Sbjct: 305 AMTPKGAYFANIAAIVAAMAVSFVVAAVLLKTSKVKEEDDIEAATRRMHDMKAESKGGAT 364

Query: 370 ALEAEQAKAEEASELSPESVNKIIFACDAGMGSSAMGASILRNKVKKAEL-DISVTNTAI 428
            L    A  + A++LS   V KII ACDAGMGSSAMGA +LR KV+ A L +ISVTN AI
Sbjct: 365 PL----AAGDVANDLS--HVRKIIVACDAGMGSSAMGAGVLRKKVQDAGLSNISVTNCAI 418

Query: 429 NNLPSDADIVITHKDLTDRAKAKLPNATHISVDNFLNSPKYDELIEKL 476
           NNLP D D+VITH+DLT+RA  ++P A HIS+ NFL+S  Y  L E+L
Sbjct: 419 NNLPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERL 466


Lambda     K      H
   0.320    0.136    0.383 

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: 826
Number of extensions: 33
Number of successful extensions: 4
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: 478
Length of database: 636
Length adjustment: 36
Effective length of query: 442
Effective length of database: 600
Effective search space:   265200
Effective search space used:   265200
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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