Alignments for a candidate for mtlA in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

Alignments for a candidate for mtlA in Salinicoccus carnicancri Crm

Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_017549667.1 C792_RS0111845 PTS mannitol transporter subunit IICBA

Query= BRENDA::P00550
         (637 letters)



>NCBI__GCF_000330705.1:WP_017549667.1
          Length = 591

 Score =  524 bits (1350), Expect = e-153
 Identities = 275/502 (54%), Positives = 351/502 (69%), Gaps = 18/502 (3%)

Query: 3   SDIKIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPL 62
           S I  KVQ+FG FLS+M+MPNI AFIAWG+ITA+FI  GW PNE LA +V PMI YLLPL
Sbjct: 6   SGISRKVQAFGSFLSSMIMPNIAAFIAWGLITAMFIDVGWFPNEDLATMVDPMIVYLLPL 65

Query: 63  LIGYTGGKLVGGERGGVVGAITTMGVIVG-ADMPMFLGSMIAGPLGGWCIKHFDRWVDGK 121
           LI YTGGKL+   RGGVVGA  TMGVI    D PM LG+M+ GPLGG+ +K  D  +  +
Sbjct: 66  LIAYTGGKLISDVRGGVVGATATMGVIAAFPDSPMLLGAMVMGPLGGYLMKQVDAVLVPR 125

Query: 122 IKSGFEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFV 181
           I+ G EMLVNNFSAG +   LA+  + G+GP+V  L+++L   V+ +V   +LP+ASIF+
Sbjct: 126 IRQGLEMLVNNFSAGFLAFFLALFGYYGLGPVVSWLTQLLGRLVDVIVDAGLLPIASIFI 185

Query: 182 EPAKILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQ 241
           EPAK+LFLNNAINHG+ +PL  ++  E+G+SI F +E+NPGPG G+LLAYM FG+G+A+ 
Sbjct: 186 EPAKVLFLNNAINHGVLTPLASEEVREVGRSILFTLESNPGPGFGILLAYMIFGKGTARA 245

Query: 242 SAGGAAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSIL 301
           +A GAAIIHF+GGIHEIYFPY+LM P L++A ILGG +G+ T ++L  GL  PA+PGSIL
Sbjct: 246 TAPGAAIIHFVGGIHEIYFPYILMKPTLVVAAILGGASGILTFSLLDFGLSGPAAPGSIL 305

Query: 302 AVLAMTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKAESKG 361
           A +AMTP+G Y     G+ AA  VSF+V+A +LK SK K+E D+EAAT +M+    ESKG
Sbjct: 306 AYIAMTPRGEYLTMFLGILAATLVSFLVAAAILKFSKQKDEADLEAATAQME----ESKG 361

Query: 362 ASPLSAGDVTN-----------DLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQI 410
                AG +T            D  +V KI+ ACDAGMGSSAMGAG+L+ K + AGL  I
Sbjct: 362 KKSSVAGSLTKTEDAETTEAGVDYKNVDKIVFACDAGMGSSAMGAGMLKNKFKKAGL-DI 420

Query: 411 SVTNSAINNLPPDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQR 470
            VTNSAIN L  D D++IT + LTERA  +VP A+HIS+ NFL+S  Y  L E L   Q 
Sbjct: 421 EVTNSAINQLKGDEDIIITQKTLTERAENKVPTAKHISVDNFLNSPKYDELLEELKEEQG 480

Query: 471 HTANEEKVKDSLKDSFDDSSAN 492
            +  EE   +S    FD S  +
Sbjct: 481 PSQTEEST-ESEPAGFDYSKVD 501



 Score =  106 bits (265), Expect = 3e-27
 Identities = 57/97 (58%), Positives = 70/97 (72%), Gaps = 1/97 (1%)

Query: 373 DLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAINNLPPDVDLVITHRD 432
           D S V K++ ACDAGMGSSAMGAG+L+ K + AGL  I+VTNSAIN L  D D++IT + 
Sbjct: 496 DYSKVDKVVFACDAGMGSSAMGAGMLKNKFKKAGLD-INVTNSAINQLKGDEDIIITQKT 554

Query: 433 LTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQ 469
           LTERA  +VP A+HIS+ NFL+S  Y  LTE L   Q
Sbjct: 555 LTERAENKVPTAKHISVDNFLNSPHYDELTEELKKRQ 591


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: 926
Number of extensions: 41
Number of successful extensions: 6
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: 591
Length adjustment: 37
Effective length of query: 600
Effective length of database: 554
Effective search space:   332400
Effective search space used:   332400
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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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