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.
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:
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