GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cmtA in Escherichia coli BW25113

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 17660 b3599 fused mannitol-specific PTS enzymes: IIA components/IIB components/IIC components (NCBI)

Query= TCDB::P42956
         (478 letters)



>lcl|FitnessBrowser__Keio:17660 b3599 fused mannitol-specific PTS
           enzymes: IIA components/IIB components/IIC components
           (NCBI)
          Length = 637

 Score =  588 bits (1515), Expect = e-172
 Identities = 299/468 (63%), Positives = 367/468 (78%), Gaps = 9/468 (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  GYTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKS 124

Query: 131 GFEMLINNFTAGIVGAALTILAFYAIGPVVLTLNKLLAAGVEVIVHANLLPVASVFVEPA 190
           GFEML+NNF+AGI+G  L ILAF  IGP+V  L+K+LAAGV  +V  ++LP+AS+FVEPA
Sbjct: 125 GFEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPA 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   GLV+ ASPGSI+A++
Sbjct: 245 GAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVL 304

Query: 311 AMTPRGGYFGVLAGVLVAAAVSFIVSAVILKSSKASEE-DLAAATEKMQSMKGKKSQAAA 369
           AMTP+G YF  +AGV  A AVSF+VSA++LK+SK  EE D+ AAT +MQ MK  +S+ A+
Sbjct: 305 AMTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKA-ESKGAS 363

Query: 370 ALEAEQAKAEEASELSPESVNKIIFACDAGMGSSAMGASILRNKVKKAEL-DISVTNTAI 428
            L A     +  ++LS   V KII ACDAGMGSSAMGA +LR K++ A L  ISVTN+AI
Sbjct: 364 PLSA----GDVTNDLS--HVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAI 417

Query: 429 NNLPSDADIVITHKDLTDRAKAKLPNATHISVDNFLNSPKYDELIEKL 476
           NNLP D D+VITH+DLT+RA  ++P A HIS+ NFL+S  Y  L E+L
Sbjct: 418 NNLPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERL 465


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: 40
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: 637
Length adjustment: 36
Effective length of query: 442
Effective length of database: 601
Effective search space:   265642
Effective search space used:   265642
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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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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