Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF4500 PS417_23035 PTS mannose transporter subunit IIC
Query= reanno::pseudo5_N2C3_1:AO356_07335 (954 letters) >FitnessBrowser__WCS417:GFF4500 Length = 838 Score = 512 bits (1318), Expect = e-149 Identities = 308/672 (45%), Positives = 404/672 (60%), Gaps = 28/672 (4%) Query: 284 SARIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQ 343 S + L NA+GLHARPA + AQ AK F+ I + Q + +AKSL +++L +G Sbjct: 169 SKPLTLPNANGLHARPAAVFAQAAKGFNASIYLH---KQTQSANAKSLVAIMALQTVQGD 225 Query: 344 VLEFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLI 403 L+ A A A+ AL+A + EG GE V + P A + S +L+ Sbjct: 226 TLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEPVATQS--------------SATLL 271 Query: 404 QAVAAAPGIAIGPAHIQVLQAIDYPL----RGESAAIERERLQNALNQVRSDIQGLIERA 459 + V A+PG A G QV+Q D L +G A ER L L +Q L ++A Sbjct: 272 RGVCASPGSAFG----QVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKA 327 Query: 460 KAKAIREIFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLAE 519 A EIF HQE+L+DP L + L G+SA AW A + L +AL+AE Sbjct: 328 AGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAE 387 Query: 520 RAADLRDVGRRVLAQLCGVETPN-EPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGA 578 RAADL DVG+RVL + G++ + + IL+ +++ PS A LD +V G +T GGA Sbjct: 388 RAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGA 447 Query: 579 TAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTR 638 T+H AI+ARALG+PA+ G A VL LA G +LLD +G LH++P+ A +++ + R + Sbjct: 448 TSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQ 507 Query: 639 EQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQ 698 R + Q PA TRDGH VEV AN+ V A+ G EG+GLLR+E +++ ++ Sbjct: 508 VLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNR 567 Query: 699 APDEATQEAEYRKVLDGLAG-RPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQ 757 AP Q Y + L R LVVRTLDVGGDKPL Y P+ E NPFLG+RGIRL L+ Sbjct: 568 APSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLE 627 Query: 758 RPQVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIMI 816 RPQ++ Q RA+L SA L IM PMV + E AR + E L + + +L +LGIMI Sbjct: 628 RPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMI 687 Query: 817 EVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVR 876 EVPSAAL+A V A VDFFS+GTNDLTQYTLA+DR HP L+ QAD HPAVL+LI TV+ Sbjct: 688 EVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVK 747 Query: 877 AAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQ 936 AAHAHGKWVGVCG LA++ LAVPVL+GLGVDELSVS I +KA VREL LA Q +A+ Sbjct: 748 AAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIAR 807 Query: 937 AALAVGSADDVR 948 L + A +VR Sbjct: 808 QVLGLEEAAEVR 819 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: 1489 Number of extensions: 69 Number of successful extensions: 5 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: 954 Length of database: 838 Length adjustment: 43 Effective length of query: 911 Effective length of database: 795 Effective search space: 724245 Effective search space used: 724245 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