Alignments for a candidate for treEIIA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas simiae WCS417

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate GFF4493 PS417_22995 PTS N-acetyl-D-glucosamine transporter

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



>FitnessBrowser__WCS417:GFF4493
          Length = 836

 Score =  663 bits (1711), Expect = 0.0
 Identities = 387/834 (46%), Positives = 523/834 (62%), Gaps = 24/834 (2%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L L APLSG +L L  VPD VF+S  +GDG+ IDP +  L AP  GVI ++  +GHA++I
Sbjct: 8   LTLSAPLSGPVLTLGNVPDEVFASGAMGDGIAIDPLNDCLYAPCDGVIIHVARTGHALTI 67

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
             +NG +VLMH+G+DTV L G+GF  LV++G RV  GQ L++FD D +A   +SL++L++
Sbjct: 68  RAENGAEVLMHVGIDTVELNGEGFALLVKDGARVSKGQALVQFDLDRIARQCKSLVSLII 127

Query: 127 VVSGEPFSL--LADGLVETGQPLLQL---SPSGAVEAVDEEEGDALFSKPLTLPNANGLH 181
           + +GE F L  +A   V+ G+PLLQ+   S +    AVD  E D   S  +T  +  GLH
Sbjct: 128 LTNGERFELRAVAGQKVKVGEPLLQIVARSAAAVQTAVDNSEADVSASVRIT--HRGGLH 185

Query: 182 ARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIK 241
           ARPAA+  + A+ F++   LH   +SA+  SL+ +M L   +GD ++V+  G+DAEAA++
Sbjct: 186 ARPAALIRKTAQDFSSQAQLHFGDKSASCDSLIGLMGLGIGEGDEVRVTCRGKDAEAALQ 245

Query: 242 ALVALLAEGCGEA--VVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQG 299
           ALVA L+    E   V  VA P    + A +L+GVCA+PG   G + ++T  EL   + G
Sbjct: 246 ALVAALSAVIKEEHHVPVVAPPRRAHTEAGVLQGVCAAPGLVCGPLFRLTGIELP-ADVG 304

Query: 300 TGGATERAALTRGLLAANEALQVLQDKAAGSAQA------EIFRAHQELLEDPTLLEHAH 353
              A E+  L     A  +    ++   A + Q       +IF AH  LLEDP LLE A 
Sbjct: 305 NHSADEQ--LQHLDTALEQVRSEIRSTLAHARQRKNVEEEDIFAAHLALLEDPNLLEAAT 362

Query: 354 RLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAW-- 411
           R + +G +A  AW  A  A   +   LG  L AERA DL D+ QRVL+ +LG    AW  
Sbjct: 363 RSIEQGSAATHAWRDAIQAQCAVLLALGKPLFAERANDLRDLQQRVLRALLG---EAWHF 419

Query: 412 DLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVL 471
           +LP  +I+ A +LTPS    L  +  +G     GGATSHVAILAR  GLP +  + A+VL
Sbjct: 420 ELPAGSIVSAHELTPSDLLQLSAQHAVGICMAEGGATSHVAILARGKGLPCVVALGAEVL 479

Query: 472 ALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVE 531
            +  G++V+LDA  G L LEP  A   ++   R  Q LR Q+  AQA  PA T DG  +E
Sbjct: 480 DVPQGQRVVLDAVNGRLELEPTEARHAEVHQIRDAQKLRRQQQQAQAQEPARTTDGVSIE 539

Query: 532 VTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNL 591
           V ANVAS  E + A   G +GVGLLR+EFL++DR  AP  +EQ   Y A+  A+G ++++
Sbjct: 540 VAANVASSAEAQVAFENGADGVGLLRTEFLFVDRRTAPDEQEQRHAYQAVLDAMG-DKSV 598

Query: 592 VVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIM 651
           ++RT+DVGGDK L Y+P+  E NP LGLRGIR+   RP+LL +Q RA+L  +   R  I+
Sbjct: 599 IIRTIDVGGDKQLDYLPLPVEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLERCRIL 658

Query: 652 LPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTN 711
           LPMVS + EL   R+ L+E  + L LT+ P+LG+MIEVP+AALMA+  A H DF SIGTN
Sbjct: 659 LPMVSEVDELLQIRQRLDELCVELELTQRPELGVMIEVPAAALMAEHLAKHADFLSIGTN 718

Query: 712 DLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPV 771
           DL+QYTLAMDRDH  LA + D+ HPA+LRLIA T   A  HG+WVGVCGALAS+ LA PV
Sbjct: 719 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGATKHGRWVGVCGALASDPLATPV 778

Query: 772 LIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           L+GLGV ELSVS P I  IK  VR LD A C+ +++ +L L  A  VR+A + +
Sbjct: 779 LVGLGVSELSVSPPQIAEIKDRVRHLDAAQCRQLSQGLLDLSSAKAVRQACQHH 832


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: 1519
Number of extensions: 66
Number of successful extensions: 7
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: 836
Length adjustment: 42
Effective length of query: 796
Effective length of database: 794
Effective search space:   632024
Effective search space used:   632024
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