GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Pseudomonas simiae WCS417

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

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



>FitnessBrowser__WCS417:GFF4493
          Length = 836

 Score = 1214 bits (3142), Expect = 0.0
 Identities = 623/838 (74%), Positives = 704/838 (84%), Gaps = 2/838 (0%)

Query: 1   MHNNNKDLTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVAR 60
           M  NN +LTLSAPLSGPVLTL  VPD VFASGAMGDGIAIDPLN+ L+APC GV++HVAR
Sbjct: 1   MSYNNNELTLSAPLSGPVLTLGNVPDEVFASGAMGDGIAIDPLNDCLYAPCDGVIIHVAR 60

Query: 61  TGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCK 120
           TGHA+T+RA+NGAE+L+H+G+DTVEL GEGF++LVK+G RVS GQAL++FDLD++A+ CK
Sbjct: 61  TGHALTIRAENGAEVLMHVGIDTVELNGEGFALLVKDGARVSKGQALVQFDLDRIARQCK 120

Query: 121 SLVSLLVLTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIH 180
           SLVSL++LTN E F++  +  + VKVGEPLL IV R+  + Q   D+S A+V   +RI H
Sbjct: 121 SLVSLIILTNGERFELRAVAGQKVKVGEPLLQIVARSAAAVQTAVDNSEADVSASVRITH 180

Query: 181 RGGLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADA 240
           RGGLHARPAALIR+TA  F+S++QLHF  KSASCDSLIGLMGLGIGE DEV+V+C+G DA
Sbjct: 181 RGGLHARPAALIRKTAQDFSSQAQLHFGDKSASCDSLIGLMGLGIGEGDEVRVTCRGKDA 240

Query: 241 KAALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQLAAIP 300
           +AALQAL+ ALS  + ++ H     P   R    EAGVL GVCAAPGLV GPLF+L  I 
Sbjct: 241 EAALQALVAALSAVIKEEHHVPVVAP--PRRAHTEAGVLQGVCAAPGLVCGPLFRLTGIE 298

Query: 301 LPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALL 360
           LP D G H+A+EQLQ LD ALEQVRSEIR TL+HA++ K+ EEE IFAAHLALLEDP LL
Sbjct: 299 LPADVGNHSADEQLQHLDTALEQVRSEIRSTLAHARQRKNVEEEDIFAAHLALLEDPNLL 358

Query: 361 EAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWH 420
           EAA +SI+QGSAATHAW  +I+AQC VL  LG PL AERANDLRDL+QRVLRALLG+ WH
Sbjct: 359 EAATRSIEQGSAATHAWRDAIQAQCAVLLALGKPLFAERANDLRDLQQRVLRALLGEAWH 418

Query: 421 YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASL 480
           +++PAG+IV+AHELTPSDLLQLS Q   G+CMAEGGATSHVAILARGKGLPC+VAL A +
Sbjct: 419 FELPAGSIVSAHELTPSDLLQLSAQHAVGICMAEGGATSHVAILARGKGLPCVVALGAEV 478

Query: 481 LQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRI 540
           L  PQGQ VVLDA  GRLEL P   R  +V Q +     RR++QQAQA  PA T DG+ I
Sbjct: 479 LDVPQGQRVVLDAVNGRLELEPTEARHAEVHQIRDAQKLRRQQQQAQAQEPARTTDGVSI 538

Query: 541 EVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSV 600
           EVAANVASS EA  A + GADGVGLLRTEFLFVDR+TAPDEQEQR AYQAVLDAMGDKSV
Sbjct: 539 EVAANVASSAEAQVAFENGADGVGLLRTEFLFVDRRTAPDEQEQRHAYQAVLDAMGDKSV 598

Query: 601 IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRIL 660
           IIRTIDVGGDKQLDYLPLP EANPVLGLRGIRMAQVRPELLDQQLRALLQVSPL+RCRIL
Sbjct: 599 IIRTIDVGGDKQLDYLPLPVEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLERCRIL 658

Query: 661 LPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTN 720
           LPMV+EVDELL IRQRLD LC EL LTQR ELGVMIEVPAAAL+AE LA+HADFLSIGTN
Sbjct: 659 LPMVSEVDELLQIRQRLDELCVELELTQRPELGVMIEVPAAALMAEHLAKHADFLSIGTN 718

Query: 721 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPV 780
           DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTC GA KH RWVGVCGALASDPLATPV
Sbjct: 719 DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGATKHGRWVGVCGALASDPLATPV 778

Query: 781 LIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQHWPLS 838
           L+GLG+SELSVSPPQ+ EIK+RVR LDAA CR+ S  LL+LSSA AVR AC  HWPLS
Sbjct: 779 LVGLGVSELSVSPPQIAEIKDRVRHLDAAQCRQLSQGLLDLSSAKAVRQACQHHWPLS 836


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: 1940
Number of extensions: 74
Number of successful extensions: 3
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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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