Alignments for a candidate for cmtA in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

Alignments for a candidate for cmtA in Salinicoccus carnicancri Crm

Align PTS system, mannitol-specific IICBA component aka EIICBA-Mtl aka Mannitol-permease IIABC component aka Phosphotransferase enzyme II, CBA component aka EC 2.7.1.69 aka EII-Mtl, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF (characterized)
to candidate WP_017549667.1 C792_RS0111845 PTS mannitol transporter subunit IICBA

Query= TCDB::P42956
         (478 letters)



>NCBI__GCF_000330705.1:WP_017549667.1
          Length = 591

 Score =  599 bits (1544), Expect = e-176
 Identities = 302/476 (63%), Positives = 374/476 (78%), Gaps = 4/476 (0%)

Query: 6   QQQGGMKVKVQRFGSYLSGMIMPNIGAFIAWGIITALFIPAGWFPNEQLNTLVSPMITYL 65
           +Q+ G+  KVQ FGS+LS MIMPNI AFIAWG+ITA+FI  GWFPNE L T+V PMI YL
Sbjct: 3   EQKSGISRKVQAFGSFLSSMIMPNIAAFIAWGLITAMFIDVGWFPNEDLATMVDPMIVYL 62

Query: 66  LPLLIAYTGGKMIYDHRGGVVGATAAIGVIVG-SDIPMFLGAMIMGPLGGYLIKQTDKLF 124
           LPLLIAYTGGK+I D RGGVVGATA +GVI    D PM LGAM+MGPLGGYL+KQ D + 
Sbjct: 63  LPLLIAYTGGKLISDVRGGVVGATATMGVIAAFPDSPMLLGAMVMGPLGGYLMKQVDAVL 122

Query: 125 KDKVKQGFEMLINNFTAGIVGAALTILAFYAIGPVVLTLNKLLAAGVEVIVHANLLPVAS 184
             +++QG EML+NNF+AG +   L +  +Y +GPVV  L +LL   V+VIV A LLP+AS
Sbjct: 123 VPRIRQGLEMLVNNFSAGFLAFFLALFGYYGLGPVVSWLTQLLGRLVDVIVDAGLLPIAS 182

Query: 185 VFVEPAKVLFLNNAINHGILSPIGIEQASQTGKSILFLVEANPGPGLGILLAYMFFGKGS 244
           +F+EPAKVLFLNNAINHG+L+P+  E+  + G+SILF +E+NPGPG GILLAYM FGKG+
Sbjct: 183 IFIEPAKVLFLNNAINHGVLTPLASEEVREVGRSILFTLESNPGPGFGILLAYMIFGKGT 242

Query: 245 SKSTAPGAAIIHFFGGIHEIYFPYILMKPALILAAIAGGASGLLTFTIFNAGLVAAASPG 304
           +++TAPGAAIIHF GGIHEIYFPYILMKP L++AAI GGASG+LTF++ + GL   A+PG
Sbjct: 243 ARATAPGAAIIHFVGGIHEIYFPYILMKPTLVVAAILGGASGILTFSLLDFGLSGPAAPG 302

Query: 305 SIIALMAMTPRGGYFGVLAGVLVAAAVSFIVSAVILKSSKASEE-DLAAATEKMQSMKGK 363
           SI+A +AMTPRG Y  +  G+L A  VSF+V+A ILK SK  +E DL AAT +M+  KGK
Sbjct: 303 SILAYIAMTPRGEYLTMFLGILAATLVSFLVAAAILKFSKQKDEADLEAATAQMEESKGK 362

Query: 364 KSQAAAAL-EAEQAKAEEASELSPESVNKIIFACDAGMGSSAMGASILRNKVKKAELDIS 422
           KS  A +L + E A+  EA  +  ++V+KI+FACDAGMGSSAMGA +L+NK KKA LDI 
Sbjct: 363 KSSVAGSLTKTEDAETTEAG-VDYKNVDKIVFACDAGMGSSAMGAGMLKNKFKKAGLDIE 421

Query: 423 VTNTAINNLPSDADIVITHKDLTDRAKAKLPNATHISVDNFLNSPKYDELIEKLKK 478
           VTN+AIN L  D DI+IT K LT+RA+ K+P A HISVDNFLNSPKYDEL+E+LK+
Sbjct: 422 VTNSAINQLKGDEDIIITQKTLTERAENKVPTAKHISVDNFLNSPKYDELLEELKE 477



 Score =  135 bits (341), Expect = 3e-36
 Identities = 72/123 (58%), Positives = 90/123 (73%), Gaps = 7/123 (5%)

Query: 363 KKSQAAAALEAEQ--AKAEEASELSP-----ESVNKIIFACDAGMGSSAMGASILRNKVK 415
           K  +    L+ EQ  ++ EE++E  P       V+K++FACDAGMGSSAMGA +L+NK K
Sbjct: 467 KYDELLEELKEEQGPSQTEESTESEPAGFDYSKVDKVVFACDAGMGSSAMGAGMLKNKFK 526

Query: 416 KAELDISVTNTAINNLPSDADIVITHKDLTDRAKAKLPNATHISVDNFLNSPKYDELIEK 475
           KA LDI+VTN+AIN L  D DI+IT K LT+RA+ K+P A HISVDNFLNSP YDEL E+
Sbjct: 527 KAGLDINVTNSAINQLKGDEDIIITQKTLTERAENKVPTAKHISVDNFLNSPHYDELTEE 586

Query: 476 LKK 478
           LKK
Sbjct: 587 LKK 589


Lambda     K      H
   0.320    0.136    0.383 

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: 797
Number of extensions: 28
Number of successful extensions: 4
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: 478
Length of database: 591
Length adjustment: 35
Effective length of query: 443
Effective length of database: 556
Effective search space:   246308
Effective search space used:   246308
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: 52 (24.6 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:

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