Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_008507649.1 BIBO1_RS12560 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::psRCH2:GFF3291 (960 letters) >NCBI__GCF_000182725.1:WP_008507649.1 Length = 756 Score = 304 bits (778), Expect = 2e-86 Identities = 201/564 (35%), Positives = 306/564 (54%), Gaps = 22/564 (3%) Query: 408 VNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVA 467 V G + GI +G V++ +P+++ E EL RLD AL + I ++ VA Sbjct: 183 VTGHGFNDGIGLGHVVLHEPRIVVTNLFNEDSQAELNRLDEALGSLRISIDDMLSRRDVA 242 Query: 468 ---SIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEA-LHDKLLA 523 R++ ++ D ++ + GL+AEAA +E+++S + + L D + Sbjct: 243 VEGEHREVLEAYRMFAHDRGWVRRLEEAVHNGLTAEAA-VEKVQSDTRARMVHLTDPYMR 301 Query: 524 ERAADLRDVGRRVLACLTGVEAEQAPD---EPYILVMDEVAPSDVATLNAQRVAGILTAG 580 ER +D D+ R+L L G + + + + I+V + +++ +R+ G++ Sbjct: 302 ERLSDFDDLANRLLRQLMGRDVKTIAESLAKDAIIVARSMGAAELLDYPRERLRGVVLED 361 Query: 581 GGATSHSAIIARALGIPAIVGAGPGVLGLARNT-LLLLDGERGELLVAPSGAQLEQARSE 639 G ATSH I+ARA+GIP +VG GV+ +A N +++DG+ G + + P A +E A +E Sbjct: 362 GAATSHVVIVARAMGIP-VVGQAKGVVSMAENNDAIIVDGDEGIVHLRPQ-ADVESAYAE 419 Query: 640 RAA-REERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVF 698 + R R+ E R A+T+DG + + N G + P+ A GA GIGL RTEL F Sbjct: 420 KVRFRARRQAHYRELRDKPAITKDGVDIALLMNAGLLVDLPQLSASGAAGIGLFRTELQF 479 Query: 699 MNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPA-EENPFLGVRGI 757 M S P QE YR V++A +P+ RTLD+GGDK LPY+ A EENP LG R I Sbjct: 480 MVASTFPRSEQQERLYRSVIDAAGDKPVTFRTLDIGGDKVLPYFRATAQEENPALGWRAI 539 Query: 758 RLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDR-------LRVEL 810 RL+L RP +L TQLRALL +A GR L++M PMV + E + A+ +++R L Sbjct: 540 RLTLDRPGLLRTQLRALLKAAGGRELKLMLPMVTEVSEVKAAREIIEREVRHLSRFAHSL 599 Query: 811 PVADLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHP 870 P+ L++G M+E+P+ L VDF S+G+NDL Q+ +A DRG+ +S + D L P Sbjct: 600 PLC-LKLGAMVEVPALLWQLDELMTAVDFVSVGSNDLFQFLMAADRGNSLISDRFDQLSP 658 Query: 871 AVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRE 930 + LR + V+A H K V +CGE+A L L+GLG +S+SA +I VKA + Sbjct: 659 SFLRALRHIVKAGARHDKPVTLCGEMAGRPLTAMTLIGLGFRSISMSAAAIGPVKAMLGA 718 Query: 931 LDFAACQRLAQQALMLP-GAHEVR 953 LD L + L P AH +R Sbjct: 719 LDAGKLNALLLEELNKPNNAHSLR 742 Lambda K H 0.317 0.134 0.384 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: 1386 Number of extensions: 74 Number of successful extensions: 6 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: 960 Length of database: 756 Length adjustment: 42 Effective length of query: 918 Effective length of database: 714 Effective search space: 655452 Effective search space used: 655452 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 24 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