GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlA in Gracilibacillus halophilus YIM-C55.5

Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_003463408.1 J416_RS01585 PTS mannitol transporter subunit IICB

Query= BRENDA::P00550
         (637 letters)



>NCBI__GCF_000359605.1:WP_003463408.1
          Length = 473

 Score =  530 bits (1364), Expect = e-155
 Identities = 268/466 (57%), Positives = 340/466 (72%), Gaps = 5/466 (1%)

Query: 6   KIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLIG 65
           + KVQ FG  LS M+MPNI AFIAWG+ITALFIP G+ PNE LA LVGPMI YLLPLLIG
Sbjct: 7   RAKVQRFGSHLSGMIMPNIAAFIAWGLITALFIPDGYFPNEELASLVGPMINYLLPLLIG 66

Query: 66  YTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKSG 125
           +TGG+LV   RGGVVGA  T+GVIVGAD+PMFLG+M  GPLGG+ IK  D     KI  G
Sbjct: 67  FTGGRLVYDIRGGVVGATATIGVIVGADIPMFLGAMAMGPLGGYLIKKLDDVFQDKIGQG 126

Query: 126 FEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPAK 185
           FEML NNFSAGI+G +LA ++   IGPI+  ++++L AGV F++   +LPLA+I +EPAK
Sbjct: 127 FEMLYNNFSAGILGAVLAGISLKIIGPIINGITQVLIAGVEFLINVGLLPLANIIIEPAK 186

Query: 186 ILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAGG 245
           +LFLNNAINHGI SP+  +QS E GKSI FL+E NPGPG+GVLLA+M FG G+A+ SA G
Sbjct: 187 VLFLNNAINHGILSPIAAEQSSETGKSILFLLETNPGPGLGVLLAFMVFGTGAARSSASG 246

Query: 246 AAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVLA 305
           A+IIHF GGIHEIYFPY+LM P L+LAVI GG++GVFT TI   GL +  SPGSI+A++ 
Sbjct: 247 ASIIHFFGGIHEIYFPYILMKPALLLAVIGGGVSGVFTYTIFNAGLTATPSPGSIVALML 306

Query: 306 MTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKAESKGASPL 365
           MTP G +F    GV  A  VSF++++++LK S   E +D+  AT +M++MK +   AS  
Sbjct: 307 MTPPGDHFIIALGVIVATLVSFLIASVILKASN-SEGEDLSKATSQMEEMKGKKSKASDS 365

Query: 366 SAGD----VTNDLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAINNLP 421
             G+     T     V K++ ACDAGMGSSAMGA +L+ K + A +  I VTN AIN+L 
Sbjct: 366 LRGNEEQASTQQAEDVNKVVFACDAGMGSSAMGASLLKDKFKKADIEGIDVTNKAINDLT 425

Query: 422 PDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVA 467
            + D++ITH+DLT+RA  ++P A+HIS+ NFL+S  Y  L  RL A
Sbjct: 426 DEADIIITHKDLTDRAKEKIPSAEHISVENFLNSPKYDELVNRLKA 471


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: 800
Number of extensions: 41
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: 473
Length adjustment: 36
Effective length of query: 601
Effective length of database: 437
Effective search space:   262637
Effective search space used:   262637
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 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