GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4832
          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:

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