Alignments for a candidate for mtlA in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mtlA in Mycolicibacterium vanbaalenii PYR-1

Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_011782706.1 MVAN_RS28100 PTS mannitol transporter subunit IICBA

Query= BRENDA::P00550
         (637 letters)



>NCBI__GCF_000015305.1:WP_011782706.1
          Length = 658

 Score =  623 bits (1607), Expect = 0.0
 Identities = 329/649 (50%), Positives = 431/649 (66%), Gaps = 30/649 (4%)

Query: 5   IKIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWL---------PNETLAKL---- 51
           ++++VQ  G  LSNMVMPNIGAFIAWG+ITALFI  GWL         P+  +AK+    
Sbjct: 15  VRVRVQKLGTALSNMVMPNIGAFIAWGLITALFIEQGWLQGIFAELKNPDGWVAKIGGWG 74

Query: 52  -------VGPMITYLLPLLIGYTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAG 104
                  VGPMITYLLP+LIGYTGG++V G RG VVGAI TMGV+ GAD+PMFLG+MI G
Sbjct: 75  AYDGAGIVGPMITYLLPVLIGYTGGRMVHGNRGAVVGAIATMGVVTGADVPMFLGAMIMG 134

Query: 105 PLGGWCIKHFDRWVDGKIKSGFEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAG 164
           PLGGWC+K  D   +GKI+ GFEMLV+NFSAGI+G+ILA+  F GIGPIV + ++     
Sbjct: 135 PLGGWCMKKLDALWEGKIRPGFEMLVDNFSAGILGLILAVFGFFGIGPIVSSFTRAAGNA 194

Query: 165 VNFMVVHDMLPLASIFVEPAKILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPG 224
           V+F+V +D+LPL SI +EPAK+LFLNNAINHG+ +PLG  Q+ E GKSI FL+EANPGPG
Sbjct: 195 VDFLVENDLLPLTSILIEPAKVLFLNNAINHGVLTPLGTTQALETGKSILFLLEANPGPG 254

Query: 225 MGVLLAYMFFGRGSAKQSAGGAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTL 284
           +G+LLAYM FGRG A+ SA GAAII F GGIHEIYFPYVLM P+LI+A ILGGMTGVF  
Sbjct: 255 LGLLLAYMAFGRGLARASAPGAAIIQFFGGIHEIYFPYVLMKPKLIVATILGGMTGVFIN 314

Query: 285 TILGGGLVSPASPGSILAVLAMTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDD 344
            + G GL +PA+PGSI+AV A T  G++      V  + AVSF V+A+LLKT +  +E D
Sbjct: 315 VLFGSGLRAPAAPGSIIAVYAQTASGSFLGVTLSVFGSAAVSFAVAALLLKTDRATDESD 374

Query: 345 IEAATRRMQDMKAESKGASPLSAGDVTNDLSHVRKIIVACDAGMGSSAMGAGVLRKKIQD 404
           + AAT  M+ +K +    S ++   V      +R I+ ACDAGMGSSAMGA VLR+KIQ 
Sbjct: 375 LAAATAEMESLKGKK---SSVAGALVATSTGPIRSIVFACDAGMGSSAMGASVLRRKIQQ 431

Query: 405 AGLSQISVTNSAINNLPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTER 464
           AG   + VTNSAI+NL    DLVI+HRDLT RA ++   A H+S+ +F+ S  Y  + ER
Sbjct: 432 AGFGDVKVTNSAISNLSDTYDLVISHRDLTARARQRTGSAVHVSVDDFMGSPRYDEIVER 491

Query: 465 LVAAQRHTANEEKVKDSLKDSFDDSSANLFKLGAENIFLGRKAATKEEAIRFAGEQLVKG 524
           L   Q +T   +    ++++  +  + ++  L   +I L   A T  +AI  AG  LV  
Sbjct: 492 L--KQTNTGGGDGAPAAVEEPAEAPADDVLPL--SSIVLDGAATTAADAITEAGRLLVTA 547

Query: 525 GYVEPEYVQAMLDREKLTPTYLGESIAVPHGTVEAKDRVLKTGVVFCQYPEGVRFGEEED 584
           G VEP Y+ AM  RE    TY+G  +A+PHGT EAKD + +TG+ F +Y E + +  +  
Sbjct: 548 GAVEPAYIDAMHQRESSISTYMGNGLAIPHGTNEAKDTIRRTGLSFVRYAEPIDWNGKP- 606

Query: 585 DIARLVIGIAARNNEHIQVITSLTNALDDESVIERLAHTTSVDEVLELL 633
             A  V+GIA    +H+ ++T +         + RL   T+ +EV  +L
Sbjct: 607 --AEFVVGIAGAGKDHMALLTKIAQVFLKADDVARLREATTTEEVKAIL 653


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: 983
Number of extensions: 47
Number of successful extensions: 5
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: 658
Length adjustment: 38
Effective length of query: 599
Effective length of database: 620
Effective search space:   371380
Effective search space used:   371380
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 24 2021. 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 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