Alignments for a candidate for treEIIA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas stutzeri RCH2

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate GFF3793 Psest_3862 phosphoenolpyruvate-protein phosphotransferase

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



>FitnessBrowser__psRCH2:GFF3793
          Length = 757

 Score =  301 bits (770), Expect = 1e-85
 Identities = 189/563 (33%), Positives = 304/563 (53%), Gaps = 15/563 (2%)

Query: 273 GVCASPGSAFGQVVQVTDP---ELVITEQGTGGATERAALTRGLLAANEALQVLQDKAAG 329
           G+  +PG+  G  + V  P   ++V  +       E       L A    ++ L +K A 
Sbjct: 180 GIPGAPGAGVGTALVVLPPADLDVVPDKHIDNIDAELTLFEAALEAVRADMRNLSEKLAT 239

Query: 330 SAQAE---IFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIA 386
             + E   +F  +  +L+D  L     +++  G+ A  A        V  F+ + +A + 
Sbjct: 240 QMRKEERALFDVYLMMLDDSALGGEVTKVIRTGQWAQGALRQVVREHVRRFEMMDDAYLR 299

Query: 387 ERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGG 446
           ERA+D+ D+G+R+L  +   +      P++ IL++E+L+P+    +   K++G V+V G 
Sbjct: 300 ERASDVKDIGRRLLSYLQEARQQTLTYPDKTILVSEELSPAMLGEVPEGKLVGMVSVLGS 359

Query: 447 ATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEA-ARK 505
           + SHVAILARA+G+P + G      +  +G ++++D  +GE+   P     EQ E  A +
Sbjct: 360 SNSHVAILARAMGIPTVMGAVDLPYSKVDGIELIVDGYRGEIITNPGKVLREQYEVLAEQ 419

Query: 506 HQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDR 565
            + L    DV +  LP  T DGH + +  N   L +V  A   G EGVGL R+E  ++ +
Sbjct: 420 ERQLSEGLDVLR-ELPCETIDGHRIPLWVNTGLLADVVRAQERGAEGVGLYRTEVPFMIK 478

Query: 566 NRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLC 625
            R PS +EQ   Y     A      + +R+LD+GGDK L Y P+  E NPFLG RGIR+ 
Sbjct: 479 ERFPSEKEQMAIYREQLEAFHP-LPVTMRSLDIGGDKCLPYFPIKEE-NPFLGWRGIRVT 536

Query: 626 LERPQLLREQFRAIL-ASAGFARLHIMLPMVSLLSELHLARKILEE---EALALGL-TEL 680
           L+ P++   Q RA+L ASAG   L I+LPM+S + EL  A  ++     E    GL   +
Sbjct: 537 LDHPEIFLLQTRAMLKASAGLNNLRILLPMISGIGELEEALHLIHRAWCEVRDEGLDVHM 596

Query: 681 PKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLR 740
           P +G+MIEVP+A  +    A  VDF S+G+NDLTQY LA+DR++PR+A+  D  HPAVL 
Sbjct: 597 PPVGVMIEVPAAVYLTRELARQVDFISVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLE 656

Query: 741 LIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLA 800
            +   VK AH+ GK V +CG +A +  A  +L+ +G D LS++   +P +K  +R++ + 
Sbjct: 657 ALQRVVKEAHSEGKPVSICGEMAGDPAAAVLLLAMGFDSLSMNATNLPKVKWLLRQISMD 716

Query: 801 DCQIIARQVLGLEEAAEVREALR 823
             Q +  +V+ L+    ++  ++
Sbjct: 717 TAQQLLARVMLLDSPQVIQSTVQ 739


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: 1263
Number of extensions: 74
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: 757
Length adjustment: 41
Effective length of query: 797
Effective length of database: 716
Effective search space:   570652
Effective search space used:   570652
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: 55 (25.8 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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