Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E3

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_04460 AO353_04460 PTS N-acetyl-D-glucosamine transporter

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



>FitnessBrowser__pseudo3_N2E3:AO353_04460
          Length = 838

 Score =  661 bits (1706), Expect = 0.0
 Identities = 385/831 (46%), Positives = 522/831 (62%), Gaps = 16/831 (1%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L L APLSG +L L KVPDPVF+S  +GDG+ IDP + TL AP AGV+ ++  +GHAV++
Sbjct: 8   LTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVARTGHAVTL 67

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
             DNG ++L+H+GLDTV L G+GF+ LV+EG RV  GQ L+ FD D VA   +SL++L++
Sbjct: 68  RADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCKSLVSLLV 127

Query: 127 VVSGEPFSLLADGL--VETGQPLLQLSPSGAVEA-VDEEEGDALFSKPLTLPNANGLHAR 183
           + + E F +L   L  V+ G+PLL + P     A V+ +   A     + + +  GLHAR
Sbjct: 128 LTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIHRGGLHAR 187

Query: 184 PAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKAL 243
           PAA+  Q A  FN+   LH   +SA+  SL+ +M L   + D +QVS  G DA+AA++AL
Sbjct: 188 PAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADAKAALQAL 247

Query: 244 VALLAEGCGE-----AVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQ 298
           +  L+    +     A   +A+   T + A +L GVCA+PG   G + Q+    L   + 
Sbjct: 248 LNALSTAVNDDSHAAAPTPIAQRTRT-AEAGVLNGVCAAPGLVGGPLFQLAAIPLP-EDT 305

Query: 299 GTGGATERA-ALTRGL-LAANEALQVLQD--KAAGSAQAEIFRAHQELLEDPTLLEHAHR 354
           G   A E+  AL R L    +E  + L    K   + + +IF AH  LLEDP LLE A +
Sbjct: 306 GKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQ 365

Query: 355 LLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLP 414
            + +G +A  AW+ +  A   + Q LGN L+AERA DL D+ QRVL+ +LG QD  +D+P
Sbjct: 366 SIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLG-QDWHYDVP 424

Query: 415 ERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALA 474
             AI+ A +LTPS    L  + V G     GGATSHVAILAR  GLP +  + A +L   
Sbjct: 425 AGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQP 484

Query: 475 NGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTA 534
            G+ V+LDAD G L L P+   +EQ+  A++  + R +R  AQA  PA TRDG  +EV A
Sbjct: 485 QGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVAA 544

Query: 535 NVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVR 594
           NVAS  E   AL  G +GVGLLR+EFL++DR  AP  +EQ   Y A+  A+G ++++++R
Sbjct: 545 NVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMG-DKSVIIR 603

Query: 595 TLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPM 654
           T+DVGGDK L Y+P+ AE NP LGLRGIR+   RP+LL +Q RA+L  +   R  I+LPM
Sbjct: 604 TIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPM 663

Query: 655 VSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLT 714
           V+ + EL   R+ L+     L LT+  +LG+MIEVP+AAL+A+  A H DF SIGTNDL+
Sbjct: 664 VTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTNDLS 723

Query: 715 QYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIG 774
           QYTLAMDRDH  LA + D+ HPA+LRLIA T   A  H +WVGVCGALAS+ LA PVLIG
Sbjct: 724 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPVLIG 783

Query: 775 LGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           LG+ ELSVS P +  IK  VR+LD ADC+  +  +L L  A  VR A  Q+
Sbjct: 784 LGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQH 834


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: 1530
Number of extensions: 68
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: 838
Length adjustment: 42
Effective length of query: 796
Effective length of database: 796
Effective search space:   633616
Effective search space used:   633616
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.

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, 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