GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagF in Pseudomonas fluorescens GW456-L13

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate PfGW456L13_4832 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= reanno::pseudo3_N2E3:AO353_04460
         (838 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4832 PTS system,
           glucose-specific IIA component / Phosphotransferase
           system, phosphocarrier protein HPr /
           Phosphoenolpyruvate-protein phosphotransferase of PTS
           system (EC 2.7.3.9)
          Length = 838

 Score = 1364 bits (3530), Expect = 0.0
 Identities = 704/838 (84%), Positives = 748/838 (89%)

Query: 1   MHNNNKDLTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVAR 60
           MHNNNK+LTLSAPLSGPVLTLAKVPD VFASGAMGDGIAIDPLN+TLHAPCAGVVVHVAR
Sbjct: 1   MHNNNKELTLSAPLSGPVLTLAKVPDAVFASGAMGDGIAIDPLNDTLHAPCAGVVVHVAR 60

Query: 61  TGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCK 120
           TGHAVTLRADNGAELLLHLGLDTVELQG+GFSMLVKEG RVSNGQ LLR+DLD+VAQ CK
Sbjct: 61  TGHAVTLRADNGAELLLHLGLDTVELQGQGFSMLVKEGARVSNGQPLLRYDLDKVAQQCK 120

Query: 121 SLVSLLVLTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIH 180
           SLVSLL+LTNS+DFQ  PITLKSVKVGEPLLHI+ R    AQ + + +G EV GHIRI H
Sbjct: 121 SLVSLLILTNSQDFQARPITLKSVKVGEPLLHIIRRQGVGAQADVELAGEEVVGHIRIAH 180

Query: 181 RGGLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADA 240
           RGGLHARPAALIRQTA  F SKSQLHFAGKSA+CDSLIGLMGL IGEQ EVQVSC+G DA
Sbjct: 181 RGGLHARPAALIRQTAQGFKSKSQLHFAGKSATCDSLIGLMGLAIGEQAEVQVSCQGPDA 240

Query: 241 KAALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQLAAIP 300
           +AALQALL ALSTA+ +DSHAAAPT IAQR R AEAGVL+GVCAAPGLVGGPLF L AI 
Sbjct: 241 EAALQALLTALSTALAEDSHAAAPTTIAQRNRPAEAGVLHGVCAAPGLVGGPLFHLNAIS 300

Query: 301 LPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALL 360
           LP D G H+ ++Q Q LD AL QVRSEI  TL  AKKHK T EE IFAAHLALLEDPALL
Sbjct: 301 LPVDAGHHDPQQQQQVLDAALSQVRSEIERTLVLAKKHKDTAEEAIFAAHLALLEDPALL 360

Query: 361 EAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWH 420
           +AAIQ++ QG+AATHAWSQ+I+ QCEVLQQ G+ LLAERANDLRDL+QRVLRALLG  WH
Sbjct: 361 DAAIQTVAQGTAATHAWSQAIDVQCEVLQQTGSTLLAERANDLRDLKQRVLRALLGDTWH 420

Query: 421 YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASL 480
           YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPC+VAL ++L
Sbjct: 421 YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCMVALGSTL 480

Query: 481 LQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRI 540
           L Q QGQ VVLDADGGRLELTP ++RL  V Q Q++  QRR  QQAQAHTPA T DGLRI
Sbjct: 481 LDQQQGQPVVLDADGGRLELTPSAERLADVRQLQQQQQQRRAEQQAQAHTPALTTDGLRI 540

Query: 541 EVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSV 600
           EVAANVASS EAADAL  GADGVGLLRTEFLFVDR TAPDEQEQ  AYQAVLDAMGDKSV
Sbjct: 541 EVAANVASSTEAADALANGADGVGLLRTEFLFVDRHTAPDEQEQHHAYQAVLDAMGDKSV 600

Query: 601 IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRIL 660
           IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIR+AQ RPELLDQQLRALL + PL RCRIL
Sbjct: 601 IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRLAQARPELLDQQLRALLHLRPLSRCRIL 660

Query: 661 LPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTN 720
           LPMVTEVDELL+I QRLDALC EL L QR ELGVMIEVPAAALLAEQLAEHADFLSIGTN
Sbjct: 661 LPMVTEVDELLHIHQRLDALCGELGLAQRPELGVMIEVPAAALLAEQLAEHADFLSIGTN 720

Query: 721 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPV 780
           DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTC GAA+H RWVGVCGALASDPLATPV
Sbjct: 721 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAQHNRWVGVCGALASDPLATPV 780

Query: 781 LIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQHWPLS 838
           LIGLG+SELSVSP QVGEIK+RVR LDA++CRR S  LL LSSA+AVRHACHQHWPLS
Sbjct: 781 LIGLGVSELSVSPVQVGEIKDRVRHLDASECRRISQGLLKLSSASAVRHACHQHWPLS 838


Lambda     K      H
   0.318    0.133    0.379 

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: 2100
Number of extensions: 83
Number of successful extensions: 2
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.

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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:

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:

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:

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