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 D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_017220637.1 A923_RS0105395 phosphoenolpyruvate-protein phosphotransferase PtsI

Query= reanno::WCS417:GFF4500
         (838 letters)



>NCBI__GCF_000276805.1:WP_017220637.1
          Length = 575

 Score =  379 bits (973), Expect = e-109
 Identities = 218/572 (38%), Positives = 333/572 (58%), Gaps = 20/572 (3%)

Query: 270 LLRGVCASPGSAFGQVVQVTDPELVITEQG--TGGATERAALTRGLLAAN-------EAL 320
           ++ G+ ASPG AFG+     + E+V+ +Q   T    E+ A+    LAA        EA+
Sbjct: 1   MISGILASPGIAFGKAQLFINEEIVLNQQTIETAQIDEQIAI---FLAARDKSAIQLEAI 57

Query: 321 QVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAA-FAWNSATLATVTLFQG 379
             +  +  G  +AEIF  H  LLED  L E     + + K++A  A +S       +   
Sbjct: 58  TEMARQTFGDEKAEIFEGHMMLLEDEELEEDIVTFIKKNKASADLAIHSIIEENAEMMAA 117

Query: 380 LGNALIAERAADLADVGQRVLKLILGIQD-SAWDLPERAILIAEQLTPSQTASLDTRKVL 438
           L +  + ERAAD  D+G R++K  LG++  S   + +  ILIA  LTPS+TA ++  K+L
Sbjct: 118 LDDPYLRERAADFRDIGNRIVKNALGMEIVSLSAIEDEVILIASDLTPSETAQINLDKIL 177

Query: 439 GFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIE 498
           GFVT  GG T+H +I+AR+L LPAI G       + +G  V+LDA    + + P+ + I+
Sbjct: 178 GFVTDLGGRTAHTSIMARSLELPAIVGTGNVTEIIKSGDFVILDAINNNVIVNPSESVIK 237

Query: 499 QLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRS 558
           + +A +   +      +    LPA T DG HVEV  NV ++++    +  GGEGVGL R+
Sbjct: 238 EYQATQAQYLAEKAELLKMKDLPAITLDGKHVEVCGNVGTVKDCAGVIRNGGEGVGLYRT 297

Query: 559 EFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLG 618
           EFL++DR+  P+ +EQ   Y A+A ++  + ++++RT+D+GGDK L Y+ +  E NPFLG
Sbjct: 298 EFLFMDRDSLPTEDEQFEAYKAVAESMNGQ-SVIIRTMDIGGDKDLPYLNLPKEMNPFLG 356

Query: 619 LRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLARKIL-----EEEAL 673
            R IR+C +RP+++  Q RAIL ++ F ++ IM PM+  + E+ L + IL     E  A 
Sbjct: 357 WRAIRICFDRPEIMNAQLRAILRASAFGKIRIMFPMIISVEEIRLLKDILATLKAELTAE 416

Query: 674 ALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADS 733
                   + G+M+E P+AA +A      VDFFSIGTNDLTQYTLA+DR +  +++  + 
Sbjct: 417 GHAFDAAMETGVMVETPAAAAIAHHLIKEVDFFSIGTNDLTQYTLAVDRGNEMISDLYNP 476

Query: 734 FHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKAT 793
             PAVL LI   + A+HA GKW G+CG LA +  A  +L+G+G+DE S+S   IP +K T
Sbjct: 477 LTPAVLTLIKQVIDASHAAGKWTGMCGELAGDETATLLLLGMGLDEFSMSGISIPKVKKT 536

Query: 794 VRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           +R  + AD + +A Q L    A E++E + Q+
Sbjct: 537 IRNANFADTKELADQALSCATAGEIQELIAQF 568


Lambda     K      H
   0.318    0.133    0.371 

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: 865
Number of extensions: 31
Number of successful extensions: 6
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: 838
Length of database: 575
Length adjustment: 39
Effective length of query: 799
Effective length of database: 536
Effective search space:   428264
Effective search space used:   428264
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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