Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF4493 PS417_22995 PTS N-acetyl-D-glucosamine transporter
Query= reanno::pseudo5_N2C3_1:AO356_07335 (954 letters) >FitnessBrowser__WCS417:GFF4493 Length = 836 Score = 463 bits (1191), Expect = e-134 Identities = 281/671 (41%), Positives = 383/671 (57%), Gaps = 23/671 (3%) Query: 284 SARIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQ 343 SA + + + GLHARPA ++ + A+ F + ++ D + S SL L+ LG G Sbjct: 173 SASVRITHRGGLHARPAALIRKTAQDFSSQAQLHF---GDKSASCDSLIGLMGLGIGEGD 229 Query: 344 VLEFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLI 403 + A AL AL+AA+ + EE +P + PR A ++ Sbjct: 230 EVRVTCRGKDAEAALQALVAALSAVIKEE-HHVPVVAPPRR-----------AHTEAGVL 277 Query: 404 QAVAAAPGIAIGPAHIQVLQAIDYP--LRGESAAIERERLQNALNQVRSDIQGLIERAKA 461 Q V AAPG+ GP + L I+ P + SA + + L AL QVRS+I+ + A+ Sbjct: 278 QGVCAAPGLVCGP--LFRLTGIELPADVGNHSADEQLQHLDTALEQVRSEIRSTLAHARQ 335 Query: 462 KAIRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLA 518 + E IF H +L+DP L + ++ G +A AW I+A AL L A Sbjct: 336 RKNVEEEDIFAAHLALLEDPNLLEAATRSIEQGSAATHAWRDAIQAQCAVLLALGKPLFA 395 Query: 519 ERAADLRDVGRRVLAQLCGVETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGA 578 ERA DLRD+ +RVL L G E I+ E+ PSD+ +L GI A GGA Sbjct: 396 ERANDLRDLQQRVLRALLGEAWHFELPAGSIVSAHELTPSDLLQLSAQHAVGICMAEGGA 455 Query: 579 TAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTR 638 T+H AI+AR G+P +V GA VL + G ++LD GRL ++P A + RD + Sbjct: 456 TSHVAILARGKGLPCVVALGAEVLDVPQGQRVVLDAVNGRLELEPTEARHAEVHQIRDAQ 515 Query: 639 EQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQ 698 + R + Q EPA T DG ++EV AN+ SA A E GA+G+GLLRTE +F+ Sbjct: 516 KLRRQQQQAQAQEPARTTDGVSIEVAANVASSAEAQVAFENGADGVGLLRTEFLFVDRRT 575 Query: 699 APDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQR 758 APDE Q Y+ VLD + + +++RT+DVGGDK L Y P+ E NP LG+RGIR+ R Sbjct: 576 APDEQEQRHAYQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPVEANPVLGLRGIRMAQVR 635 Query: 759 PQVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIMIE 817 P++++ QLRALL+ + RI+ PMV VDE Q R + L +E+ + +LG+MIE Sbjct: 636 PELLDQQLRALLQVSPLERCRILLPMVSEVDELLQIRQRLDELCVELELTQRPELGVMIE 695 Query: 818 VPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRA 877 VP+AAL+A LAK DF S+GTNDL+QYTLA+DR H L+A+ D LHPA+L+LI T Sbjct: 696 VPAAALMAEHLAKHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAG 755 Query: 878 AHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQA 937 A HG+WVGVCG LA+DPLA PVLVGLGV ELSVS IAE+K RVR L AQ + L+Q Sbjct: 756 ATKHGRWVGVCGALASDPLATPVLVGLGVSELSVSPPQIAEIKDRVRHLDAAQCRQLSQG 815 Query: 938 ALAVGSADDVR 948 L + SA VR Sbjct: 816 LLDLSSAKAVR 826 Lambda K H 0.318 0.135 0.381 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: 1470 Number of extensions: 73 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 954 Length of database: 836 Length adjustment: 43 Effective length of query: 911 Effective length of database: 793 Effective search space: 722423 Effective search space used: 722423 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