Alignments for a candidate for fruII-ABC in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Mycolicibacterium vanbaalenii PYR-1

Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_011777419.1 MVAN_RS00500 PTS lactose transporter subunit IIC

Query= TCDB::Q0S1N2
         (700 letters)



>NCBI__GCF_000015305.1:WP_011777419.1
          Length = 656

 Score =  859 bits (2219), Expect = 0.0
 Identities = 459/684 (67%), Positives = 519/684 (75%), Gaps = 36/684 (5%)

Query: 14  IISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALARESQSATGLPGGIA 73
           II+ DL+ LD  +   K+ VI+ L   LA AGR  +AD L  AA+ARE QSATGLPGGIA
Sbjct: 8   IITRDLVLLDVAIDGDKQAVIARLVNALAAAGRTDDADGLIGAAMAREEQSATGLPGGIA 67

Query: 74  IPHCRSEAVVAASLGFARLAPKVDFGAPDGPADLVFLIAAPEGAGAEHMKLLSSLARALV 133
           IPHCRS  V   ++GFARL P VDFGAPDGPADL FLIAAP+  G EHMKLLSSLARALV
Sbjct: 68  IPHCRSPYVDTPTIGFARLTPGVDFGAPDGPADLAFLIAAPDSGGQEHMKLLSSLARALV 127

Query: 134 RPAFVGALRDAKTPAEIVTLVNDVLAPAPAATPAAAAPAAAAAAAPAAAAAVPAPKPEPV 193
           R  FV +LR+A +  E+V LV  V+ PAPAA PA                  P  KP   
Sbjct: 128 RKDFVESLRNAGSADEVVALVEGVVNPAPAAPPA------------------PVEKP--- 166

Query: 194 APEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQGSSGSTPLA 253
                       K IVA+TACPTGIAHTYMAAD+L AA + AGV + VETQGSSGSTPL 
Sbjct: 167 ----------AAKTIVAITACPTGIAHTYMAADALAAAAKEAGVTLVVETQGSSGSTPLP 216

Query: 254 PGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAGMNPSAAIV 313
              IAGA AVIFATDVGVK + RFAGKPVVASGVKRAINEP  MI EA+ A  NP+A  V
Sbjct: 217 SDTIAGADAVIFATDVGVKDRGRFAGKPVVASGVKRAINEPAKMIAEAVAAADNPNAPRV 276

Query: 314 DAGSAGSAADEPAGSIGWGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEISGPAE 373
           + GS  +A++ P+G +GWGT  RQ+LLTGVSYMIPFVAAGGLLIALGFL  GYEI+    
Sbjct: 277 E-GSGAAASEAPSGDVGWGTRTRQILLTGVSYMIPFVAAGGLLIALGFLFAGYEIADTGN 335

Query: 374 DIVLSNSLGQLPEGGLATYLGAVLFQLGSLAFSFLVPALAGYIAFAIADRPGLAPGFTAG 433
           DI L+NSL  LP GG   YLGA+LF LG LAF FLVPALAGYI+FAIADRPG+APGFTAG
Sbjct: 336 DIALNNSLTNLPPGGFLEYLGAILFSLGGLAFGFLVPALAGYISFAIADRPGIAPGFTAG 395

Query: 434 AVAVFVGAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMPVVIIPLFATLIVGALMFLV 493
           A+AVF+G GFIGG+VGG++AG  ALWIS + VPQW RGLMPVVI+PL A+L VG +MF +
Sbjct: 396 ALAVFIGGGFIGGIVGGVLAGFAALWISNLKVPQWFRGLMPVVIVPLGASLFVGLIMFFL 455

Query: 494 LGRPLASITSGLTNWLNGLSGSSVIFLGIILGLMMCFDLGGPVNKAAYAFAVAGLNVNDP 553
           +GRPLA I SGLTNWL+GLSG+S IFLGIILGLMMCFDLGGPVNKAAYAFA AGL     
Sbjct: 456 VGRPLALINSGLTNWLSGLSGTSAIFLGIILGLMMCFDLGGPVNKAAYAFATAGLAAETT 515

Query: 554 ASLRIMAAVMAAGMVPPLAMALASTVLRPSLFSEAERENGKAAWLLGSAFISEGAIPFAA 613
           AS  IMAAVMAAGMVPPLAMALA+T+ RP LFSE ERENG+AAWLLG++FISEGAIPFAA
Sbjct: 516 ASFEIMAAVMAAGMVPPLAMALATTI-RPGLFSEPERENGRAAWLLGASFISEGAIPFAA 574

Query: 614 ADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFFAIGNLLWFLVALAAGVVVAAL 673
           ADPLRVIPSMM GGA+TGAL MAF  T  APHGGIFV FAI N L F++AL AG V AAL
Sbjct: 575 ADPLRVIPSMMFGGAITGALCMAFGATSRAPHGGIFVLFAIDNKLGFVIALVAGTVAAAL 634

Query: 674 CVVGAKEFIKPGASDAELDPDVAT 697
            VV AK+FIK G   A+ +P++ T
Sbjct: 635 AVVAAKQFIKAG---AKTEPELVT 655


Lambda     K      H
   0.320    0.136    0.395 

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: 1371
Number of extensions: 58
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: 700
Length of database: 656
Length adjustment: 39
Effective length of query: 661
Effective length of database: 617
Effective search space:   407837
Effective search space used:   407837
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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Steps (tab-delimited)
Rules (tab-delimited)
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