Alignments for a candidate for treEIIA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Sphingomonas koreensis DSMZ 15582

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate Ga0059261_1646 Ga0059261_1646 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)

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



>FitnessBrowser__Korea:Ga0059261_1646
          Length = 830

 Score =  599 bits (1545), Expect = e-175
 Identities = 346/826 (41%), Positives = 477/826 (57%), Gaps = 10/826 (1%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L + +PL G    LD VPDPVF+ R++GDG+ I P + T+CAP  G +  + ++GHAVS+
Sbjct: 3   LIITSPLRGWAAPLDSVPDPVFAQRMMGDGVAIQPLADTVCAPFDGEVVTLHEAGHAVSL 62

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
             D G +VL+HIGLDTV L G+GFT LV  G  V  G PLI FD D VAL A SL+T ++
Sbjct: 63  RSDEGAEVLIHIGLDTVGLKGRGFTPLVAPGATVARGDPLIRFDMDAVALGATSLITPVI 122

Query: 127 VVSGEPFSLLADGL---VETGQPLLQLSPSGAVEAVDEEEGDALFSKPLTLPNANGLHAR 183
           V + E F++    +   +   + L+ L+P+        ++G  +  + +TL   +G+HAR
Sbjct: 123 VTNAEAFTITRRTMGRAIGAHEELMALAPARTQPRRWSDDGTVIEER-VTLILPHGIHAR 181

Query: 184 PAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKAL 243
           PAA   + A+ F A I+L    +  +A+S V ++AL T  GD L V A G DAEAA+ A+
Sbjct: 182 PAARLGECARQFEAEIHLLHGDKRGDARSTVGLLALGTRLGDELVVQARGSDAEAALAAI 241

Query: 244 VALLAEGCGEAVVNVAEPVATQSSATL----LRGVCASPGSAFGQVVQVTDPELVITEQG 299
           VALL    GE     A  +A  ++  L    + GV ASPG A G   ++    + +  +G
Sbjct: 242 VALLGSDMGEGAPAHAPAIAVPAAPVLQPGQIGGVIASPGLAMGPAARLRQTAIAVEREG 301

Query: 300 TGGATERAALTRGLLAANEALQVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLGEG 359
            G   ER AL          +    D A GS  A + RAH  LL+DP L   A   +  G
Sbjct: 302 KGVDAERTALDAARTEVRVRIGARADAAGGSVAA-VMRAHLALLDDPELAAGAETRIAAG 360

Query: 360 KSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAIL 419
            SA +AW  A    +   +  GNA + ER  DL D+ ++VL ++ GI   A  +   AIL
Sbjct: 361 NSAGYAWRGAVHDQIAALKATGNAHLIERTDDLVDIERQVLGVLTGIPAEADAIAAGAIL 420

Query: 420 IAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQV 479
           +A+ L PSQ  S+   K  G   V GG TSHVAIL   +GLPA+  +   + A+ +G  +
Sbjct: 421 VADDLLPSQLVSIAASKPAGICLVRGGPTSHVAILCAGMGLPALVAMGDAIEAIEDGTAL 480

Query: 480 LLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASL 539
           LLDA+ G +  +P+ A+ +   A    +  R     A A     T DG  +E+ AN+ ++
Sbjct: 481 LLDAEAGHVTPDPSQADADAFAARLAKREARRDAARAAAGNACQTADGVRIELFANLGTV 540

Query: 540 QEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVG 599
           ++ + A   G EG GL+RSEFL+LDR  APS +EQ   Y  IA AL   + ++VR LDVG
Sbjct: 541 EDAKAAAAQGAEGSGLVRSEFLFLDREDAPSEDEQHAAYQGIADAL-PGKPVIVRLLDVG 599

Query: 600 GDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLS 659
           GDKP AY+P DAE NP LGLRGIR+ L    LL  Q RAIL      +  IMLPMV+ +S
Sbjct: 600 GDKPAAYIPFDAEENPALGLRGIRVGLAHRDLLETQIRAILRVQPVGQCRIMLPMVASVS 659

Query: 660 ELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLA 719
           E+   R+++E     +G+    ++G+M+E P+AA+ AD+ A   DF SIGTNDLTQY LA
Sbjct: 660 EIRAVREVVERLRGEMGIETPIEVGVMVETPAAAITADLLAAEADFLSIGTNDLTQYVLA 719

Query: 720 MDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDE 779
           MDR +P +A+  D+ HPAVLR+IA T + A A G+WVGVCG LAS+  AVP+LIGLG  E
Sbjct: 720 MDRGNPAVASGVDAMHPAVLRMIAETCRRATAKGRWVGVCGGLASDPAAVPILIGLGATE 779

Query: 780 LSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           LS     +P  KA VR + LAD +  A + L    AAEVR   R +
Sbjct: 780 LSTVPGFVPEAKAIVRSVTLADARDHAERALHCSSAAEVRALARAF 825


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: 1579
Number of extensions: 70
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: 1
Length of query: 838
Length of database: 830
Length adjustment: 42
Effective length of query: 796
Effective length of database: 788
Effective search space:   627248
Effective search space used:   627248
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)
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 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