Aligments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_17540
          Length = 837

 Score =  640 bits (1650), Expect = 0.0
 Identities = 370/831 (44%), Positives = 509/831 (61%), Gaps = 17/831 (2%)

Query: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66
           L L APLSG +L L  VPD VF+S  +GDG+ IDP + TL AP    + ++  +GHAV++
Sbjct: 8   LILSAPLSGPVLTLANVPDAVFASGAMGDGIAIDPLNDTLYAPCDAEVIHVARTGHAVTL 67

Query: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126
             DNG ++L+H+GLDTV L G+GF+ LV+EG RV  GQPL+ +D D VAL  +SL++L++
Sbjct: 68  RADNGAELLLHLGLDTVELQGEGFSMLVKEGARVSHGQPLLRYDVDKVALRCKSLVSLLV 127

Query: 127 VVSGEPFSLLADGL--VETGQPLLQLSPS--GAVEAVDEEEGDALFSKPLTLPNANGLHA 182
           + +GE F      L  V+ G+PLL +     G  E  D++ G  +F + + + +  GLHA
Sbjct: 128 ITNGEHFQARPITLKGVKVGEPLLHILAKAVGQAEHHDQDSGIEVFGQ-VRIAHRGGLHA 186

Query: 183 RPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKA 242
           RPAA+  Q A+GF +   LH   +SA+  S++ +M L   +   + VS  G DAEAA++A
Sbjct: 187 RPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDAEAALQA 246

Query: 243 LVALLAEGCGE---AVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQG 299
           L+  L+    E   A     EP    +   +L GVCA+PG   G +V+++  +L     G
Sbjct: 247 LLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRLSGIQLPEDIGG 306

Query: 300 TGGATERAALTRGLLAANEALQVLQDKAAGSAQAE---IFRAHQELLEDPTLLEHAHRLL 356
                +R  L+  L      + +  + A      +   IF AH  LLEDP LL+ A   +
Sbjct: 307 HAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLDAADLFI 366

Query: 357 GEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAW--DLP 414
            +G +A  AW+ +      + Q LG+ L+AERA DL D+ QRVL+++LG    AW  D+ 
Sbjct: 367 EQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLG---EAWQFDVA 423

Query: 415 ERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALA 474
             AI+ A++LTPS    L  + V G   V GGATSHVAILAR  GLP +  +  ++LA  
Sbjct: 424 AGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQE 483

Query: 475 NGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTA 534
            G+ V+LDAD G L L P +  + Q+  A+  +     +  + A  PA T DG  VEV A
Sbjct: 484 QGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAA 543

Query: 535 NVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVR 594
           NVAS  E   +L  G +GVGLLR+EFL++DR+ AP  EEQ   Y A+  A+G ++ +++R
Sbjct: 544 NVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMG-DKPVIIR 602

Query: 595 TLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPM 654
           T+DVGGDK L Y+P+ +E NP LGLRGIRL   RP LL +Q RA+L +    R  I+LPM
Sbjct: 603 TIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPM 662

Query: 655 VSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLT 714
           V+ + EL   RK L+     LGL+E P+LG+M+EVP+AAL+A+  A H DF SIGTNDL+
Sbjct: 663 VTEVDELLHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLS 722

Query: 715 QYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIG 774
           QYTLAMDRDH  LA + D+ HPA+LRLIA T   A  HG+WVGVCGALAS+ LA PVLIG
Sbjct: 723 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIG 782

Query: 775 LGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQY 825
           LGV ELSVS P I  IK  VR LD A C  ++ ++L L  A  VR A  ++
Sbjct: 783 LGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSALAVRRACHRH 833


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: 1571
Number of extensions: 73
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: 837
Length adjustment: 42
Effective length of query: 796
Effective length of database: 795
Effective search space:   632820
Effective search space used:   632820
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, 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