Aligments for a candidate for treEIIA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for treEIIA in Desulfovibrio vulgaris Miyazaki F

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate 8501869 DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)

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



>FitnessBrowser__Miya:8501869
          Length = 846

 Score =  440 bits (1132), Expect = e-127
 Identities = 304/766 (39%), Positives = 399/766 (52%), Gaps = 61/766 (7%)

Query: 96  EGQRVEAGQPLIEFDADYVALNARSLLTLMLVVSGEPFSLLADGLVETGQPLLQLSPSGA 155
           EG    A Q  I  D D V   A+S L     + G        G+ E   P    +P+ +
Sbjct: 101 EGVMAAAVQASIGADLDTVLREAQSALAAKAELLGMALPQDGGGVDEAAPPAAGATPAAS 160

Query: 156 VEAVDEEEGDALFSKPLTLPNANGLHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVA 215
            E              L +PN  GLHARPAA    A   F A + L +  +  +A+S+  
Sbjct: 161 HELT------------LMVPNRLGLHARPAARIVTALGPFVADVQLARGERVVSARSVNR 208

Query: 216 IMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEPVATQSSA------- 268
           I  L    G+T+   AAG DAE A+KAL  L AE  G+       P AT+SS        
Sbjct: 209 IATLAVRGGETITFRAAGTDAEQALKALADLAAENFGDL------PDATKSSGRTGVEGP 262

Query: 269 ---------------TLLRGVCASPGSAFGQVV------QVTDPELVITEQGTGGATERA 307
                              GV ASPG A G  V          P+L   +  +    E A
Sbjct: 263 EGPGEQGRAGVAGVPAAKGGVPASPGIAVGPAVWHRPAFDAPPPDLAAGDPDS----EAA 318

Query: 308 ALTRGLLAANEALQVLQDKAA---GSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAA- 363
            L   L AA + L  L+ + A   G  +AEIF  H+ LL+D T+   A + + E +  A 
Sbjct: 319 RLDGALDAARKELAALERRTAAMAGKQEAEIFVMHRLLLDDATIAGDARQRIAERREPAE 378

Query: 364 FAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQ 423
            AW +        F+ L    + ERAADL DVG RVL+L+ G   S   L   ++L+A  
Sbjct: 379 AAWYAVIDQAAESFRQLPEGYMRERAADLVDVGARVLRLLTGAPPSGPRLERPSVLLAAD 438

Query: 424 LTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDA 483
           L PS  A LD   VLG VT  GGATSH AILAR++G+PA+ G  A   ++A+G  V LD 
Sbjct: 439 LGPSDMAHLDPALVLGIVTAQGGATSHAAILARSMGIPAVAGAGALAASVADGVTVALDG 498

Query: 484 DKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVE 543
             GE+ + P    +  +E+ R   +   Q  +A A+ PA T DG H+ V AN+ S  +  
Sbjct: 499 STGEVWIAPAPDVLSTIESRRASWLAVRQAALAGAARPAVTVDGRHMHVHANIGSPMDAA 558

Query: 544 HALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKP 603
            AL  G EGVGL R+EFL+LDR  AP  EEQ   Y A A A+     +VVRTLD+GGDKP
Sbjct: 559 PALQNGAEGVGLFRTEFLFLDRVAAPDEEEQRAAYVAAAAAM-PGLPVVVRTLDIGGDKP 617

Query: 604 LAYVPMDA--ETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSEL 661
           + Y+   A  E NPFLGLRGIR CL R +L   Q RA+L +A    L +M PMV+   EL
Sbjct: 618 VPYLGDFAAGEENPFLGLRGIRFCLARRELFLTQLRALLRAAAEHPLRVMFPMVAHPGEL 677

Query: 662 HLARKILEEEALALGLTELP----KLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYT 717
             A+ +LEE   AL    LP    ++GIM+EVP+A  +AD  A    FFSIGTNDL QY 
Sbjct: 678 AAAKALLEEARAALAAQGLPHGPVEVGIMVEVPAAVALADQLARESAFFSIGTNDLAQYV 737

Query: 718 LAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGV 777
           +A DR +  +A+ +D+ HPAVLR++  TV A  A G  V +CG LA  A A+P+L+GLG+
Sbjct: 738 MAADRGNAAVADLSDALHPAVLRMVRDTVAAGKAAGIPVAMCGELAGNADAIPLLVGLGL 797

Query: 778 DELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALR 823
           DELS++ P IP  K  VR  D+  C  +A + L L +AA VR  LR
Sbjct: 798 DELSMNGPAIPRAKDVVRGCDMTACVRLAGRALELPDAAAVRRLLR 843


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: 1532
Number of extensions: 50
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: 846
Length adjustment: 42
Effective length of query: 796
Effective length of database: 804
Effective search space:   639984
Effective search space used:   639984
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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