Alignments for a candidate for mtlA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for mtlA in Pseudarthrobacter sulfonivorans Ar51

Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_058930746.1 AU252_RS11000 PTS mannitol transporter subunit IICBA

Query= BRENDA::P00550
         (637 letters)



>NCBI__GCF_001484605.1:WP_058930746.1
          Length = 687

 Score =  622 bits (1605), Expect = 0.0
 Identities = 340/674 (50%), Positives = 442/674 (65%), Gaps = 47/674 (6%)

Query: 3   SDIKIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAK------------ 50
           + +++ VQ FG FLS M+MPNIGAFIAWG+ITALFI  GW+P   L              
Sbjct: 11  TSLRVHVQKFGTFLSGMIMPNIGAFIAWGLITALFIEKGWIPVPALGGFGTNAEGVPNVG 70

Query: 51  LVGPMITYLLPLLIGYTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWC 110
           LVGPMITYLLPLLI YTGG++V   RGGVVGAI TMGVIVGA +PMF+G+MI GPLGGW 
Sbjct: 71  LVGPMITYLLPLLIAYTGGRMVYDVRGGVVGAIGTMGVIVGAGIPMFIGAMIMGPLGGWT 130

Query: 111 IKHFDRWVDGKIKSGFEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVV 170
           +K  D   +GKI+ GFEMLVNNFSAGI G +LA+L F GI P+V+A S      V F+V 
Sbjct: 131 MKKIDLLWEGKIRPGFEMLVNNFSAGIWGALLAMLGFYGISPLVQAFSTAAGNVVQFLVN 190

Query: 171 HDMLPLASIFVEPAKILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLA 230
           + +LPL SIF+EPAK+LFLNNAINHG+ +PLGIQQS E GKSI FL+EANPGPGMG+LLA
Sbjct: 191 NGLLPLTSIFIEPAKVLFLNNAINHGVLTPLGIQQSLEQGKSILFLLEANPGPGMGILLA 250

Query: 231 YMFFGRGSAKQSAGGAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGG 290
           YMFFG+G AK SA GAAIIHF GGIHEIYFPYVLM P LILA I GGMTG+ TL I G G
Sbjct: 251 YMFFGKGLAKGSASGAAIIHFFGGIHEIYFPYVLMRPLLILAAIAGGMTGIATLAITGSG 310

Query: 291 LVSPASPGSILAVLAMTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATR 350
           LV+PA+PGSI+AVLA T + +Y   I  V  A +VSF+V++++LKT+K  +E D+  AT 
Sbjct: 311 LVAPAAPGSIIAVLAQTSRDSYVGVILAVVLATSVSFLVASVILKTTKHSDEVDLSDATS 370

Query: 351 RMQDMKAESKGASPL----SAGDVTNDLS-HVRKIIVACDAGMGSSAMGAGVLRKKIQDA 405
           +M+ MK +    S +     AG  T  L+  ++ I+ ACDAGMGSSAMGA VLR KI+ A
Sbjct: 371 KMEAMKGKKSSVSSVLTGAGAGVGTAVLAGPIKNIVFACDAGMGSSAMGASVLRNKIKAA 430

Query: 406 GLSQISVTNSAINNLPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERL 465
           G   + VTN+AI NL    D+VITH+DLTERA      A H S+ NF++S  Y  + E +
Sbjct: 431 GFPDVKVTNAAIANLSDTYDVVITHQDLTERAKPVTSSAAHFSVDNFMNSPRYDEIVELV 490

Query: 466 ----------------------VAAQRHTANEEKVKDSLKDSFDDSSANLFK-----LGA 498
                                  A   H A+      +   +  + +A         L A
Sbjct: 491 KEHNTEGATPDAGAAAAGAAGTAAGAGHGAHVASAPVNAAPAAGNGTAPTAVAPSDILVA 550

Query: 499 ENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLTPTYLGESIAVPHGTVE 558
           +++ L   A T++ AI  AG+ L+  G V+  Y+ AM +RE+   TY+G  +A+PHGT  
Sbjct: 551 DSVILNGTATTRDAAIDEAGQLLLARGAVDEGYLAAMHEREESVSTYMGSFLAIPHGTNA 610

Query: 559 AKDRVLKTGVVFCQYPEGVRFGEEEDDIARLVIGIAARNNEHIQVITSLTNALDDESVIE 618
           AKD +LK+ V   +YP+G+ +  ++    + V+G+A  NNEH+ +++S+     D++ + 
Sbjct: 611 AKDHILKSAVSVIRYPDGIDWNGKQ---VKFVVGVAGINNEHLHILSSIAKVFTDKAQVA 667

Query: 619 RLAHTTSVDEVLEL 632
           +L   TSV+EVLEL
Sbjct: 668 QLEAATSVEEVLEL 681


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: 1107
Number of extensions: 52
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 637
Length of database: 687
Length adjustment: 38
Effective length of query: 599
Effective length of database: 649
Effective search space:   388751
Effective search space used:   388751
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 Apr 09 2024. 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 2024 update 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