Alignments for a candidate for treEIIA in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Moritella dasanensis ArB 0140

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_017220595.1 A923_RS0105175 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>NCBI__GCF_000276805.1:WP_017220595.1
          Length = 815

 Score =  392 bits (1007), Expect = e-113
 Identities = 273/759 (35%), Positives = 401/759 (52%), Gaps = 36/759 (4%)

Query: 66  ITDDSGVQVLLHIG---LDT---VNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHAR 119
           + D+ GV VL+ +G   L T   + L     +A V+         P++E  A    + A 
Sbjct: 58  VHDEGGVLVLMDLGSALLSTEVAIELLDPEIAATVQL-----CSAPIVE-GAMAAGVAAA 111

Query: 120 SLLTLMLVVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEEGEALFSKPVHLPNP 179
           + L + +V +    +L    S L    +PV+         VV     +A  S    + NP
Sbjct: 112 ANLPIDIVRAEAMGALAGKQSHLGDEPEPVI--------AVVTSAVDKAALSTSWRVQNP 163

Query: 180 NGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAE 239
           +G+HARP+A+         A+I L ++ + ANAKSL +I  L    GD + + A G +AE
Sbjct: 164 HGIHARPSALIVATMAAIDATIELGRRDERANAKSLNSIAKLNVQCGDEICLYASGAEAE 223

Query: 240 LAISTLAQLLADGCGEAVT-PVAVVAPV-----VEAQEVSTKLLRGVCASAGSAFGYVVQ 293
           LAI+   +L     GE++   +A V  +     V +QE     L G+    G   G V+ 
Sbjct: 224 LAIAEFIRLADGHFGESIANDIASVNAISNEYSVSSQEKVEGALTGLAVCGGIVTGPVIH 283

Query: 294 VAERTLEMPEFAADQ-QLERESLERALMHATQAL-QRLRDN--AAGEAQADIFKAHQELL 349
                  +PE + +  ++E   L+ A+   T+ L Q+  D     G+  A+IFKAH  +L
Sbjct: 284 FDAVMPAIPERSFESVEMENIRLDSAIQKVTEQLVQQASDTELTLGKEHAEIFKAHMIML 343

Query: 350 EDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLI 409
            DP LL   +  + +   A  AW  AT   A  +++L ST + ER  D+ D+ ++V+  +
Sbjct: 344 ADPELLADVRLRVEQDMIAEQAWLEATALIAEQYRALKSTYMQEREADVKDIARQVMLQL 403

Query: 410 LGVPDGVW-ELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPA 468
            G   G   EL   ++L+A+ L PS TA LD  KVL     GGG TSH  ILARA+G+PA
Sbjct: 404 CGKSQGGRIELAQPSVLLAKDLLPSDTAQLDPQKVLAICLSGGGKTSHSVILARAMGIPA 463

Query: 469 VCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAA 528
           +  L   +  +  G  V +D   G L L P     ++L  +R+       ++L  A   A
Sbjct: 464 IIRLENCLELVEPGQVVTVDGFSGLLWLTPTADKQQELEERRKTWLDHTSNQLLAAQEPA 523

Query: 529 VTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIA 588
           +T DG+ F V AN+  L +   A+  GAEG+GLLR+EF++Q  +  PS  +Q   Y  IA
Sbjct: 524 MTTDGYRFNVMANIGGLEDVSAALDAGAEGVGLLRTEFMFQSHAELPSEQDQYIVYRDIA 583

Query: 589 RALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILS- 647
            ALG  R L +R+LDVGGDKPL   PM +E NPFLG+RG+RLCL    L ++Q RA+L  
Sbjct: 584 AALG-NRPLTIRSLDVGGDKPLLSYPMTAEDNPFLGLRGVRLCLADHILFKDQLRAVLRV 642

Query: 648 SAGLARLHIMLPMVSQLSELRLARLMLE--EEALALGLRELP-KLGIMIEVPAAALMADL 704
           +A  + + +M+PM++Q SEL   + ++    E L L  R+ P  +GIMIEVPAA   AD 
Sbjct: 643 AAEHSNVQLMIPMIAQPSELIAVKTLVSTCREELGLPERDYPLAIGIMIEVPAAVFNADE 702

Query: 705 FAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGV 764
            A E DFFSIGTNDLTQY +A DR +P +A   D    +V+  IA T +A       VG+
Sbjct: 703 LAQEADFFSIGTNDLTQYVMAADRGNPAVADLVDYKQQAVINAIAMTCEAGQKANIPVGM 762

Query: 765 CGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREV 803
           CG +A ++    LL+ LGV +LS S  +IP +KA +R +
Sbjct: 763 CGEMAGDSDMTELLIRLGVTKLSASASMIPGVKAKVRRI 801


Lambda     K      H
   0.318    0.132    0.370 

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: 1376
Number of extensions: 69
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: 844
Length of database: 815
Length adjustment: 42
Effective length of query: 802
Effective length of database: 773
Effective search space:   619946
Effective search space used:   619946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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