Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate RR42_RS01795 RR42_RS01795 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo5_N2C3_1:AO356_17540 (837 letters) >FitnessBrowser__Cup4G11:RR42_RS01795 Length = 591 Score = 305 bits (780), Expect = 6e-87 Identities = 205/578 (35%), Positives = 304/578 (52%), Gaps = 41/578 (7%) Query: 278 LHGVCAAPGLVTGPLVRLSGIQLPEDIGGHAIEEQR-----QRLSDALAQVRGEIHLTLE 332 LHG+ + G+ G L+ L D+ + ++E R +RL A A VR E+ +TL+ Sbjct: 5 LHGIPVSRGVAIGRAHLLAPAAL--DVSHYLVDEDRLDAEVERLRSARAAVRAEL-VTLK 61 Query: 333 HARARQHRDEEAIF-SAHLALLEDPVLLDAADLFIEQGSA-APHAWSRSIDTQCQVLQQL 390 R+ +E F H +L+D L + I A A + ++ + ++ Sbjct: 62 RDLPREAPEELGAFLDVHAMILDDEALAREPEALIRNRRYNAEWALTTRLEELMRQFDEI 121 Query: 391 GSTLLAERANDLRDLRQRVLRVLLGEAW-------------QFDVAAGAIVAAQELTPSD 437 L ER D+R + +R+L+VL G A + A G IV A +++P+D Sbjct: 122 EDEYLRERKADIRQVVERILKVLAGAAVLAPAPVPPSSLAPDGEPAPGVIVVAHDISPAD 181 Query: 438 LLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRL 497 +LQ G GG TSH AI+AR +P V + Q V++D D G + Sbjct: 182 MLQFRHTVFHGFVTDLGGRTSHTAIVARSLDIPAAVGVQSASELIRQDDWVIIDGDAGLV 241 Query: 498 ELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLAN 557 + P+ L + R Q+ R + + Q L HTPA T+DG+E+++ AN+ + +A +L Sbjct: 242 IVDPSAIILEEYRHRQSERALEKKRLQRLRHTPAVTLDGLEIDLLANIEMAEDATAALTA 301 Query: 558 GADGVGLLRTEFLFVDRH-TAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLP 616 GA GVGL R+EFLF++R PDEEEQ +AY+ ++AM PV IRTID+G DK LD Sbjct: 302 GAVGVGLFRSEFLFMNRRGELPDEEEQFEAYRGAVDAMHGLPVTIRTIDIGADKPLDGRD 361 Query: 617 --------LPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPMVT---E 665 + NP LGLR IR + P + QLRALL+ R+L+PM+ E Sbjct: 362 GRDGRGDDFETALNPALGLRAIRWSLSEPAMFLTQLRALLRASAFGPVRLLIPMLAHARE 421 Query: 666 VDELLHI----RKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDL 721 +D+ L + +++LDA G ++G M+E+PAA L+ DFLSIGTNDL Sbjct: 422 IDQTLDLIAQAKRQLDARGQ--AFDPNIKVGAMIEIPAAVLMLPLFLRRMDFLSIGTNDL 479 Query: 722 SQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLI 781 QYTLA+DR +A D LHPA+L+LIA+T A + G V VCG +A DP T +L+ Sbjct: 480 IQYTLAIDRADNAVAHLYDPLHPAVLQLIARTIREANRAGVPVAVCGEMAGDPAMTRLLL 539 Query: 782 GLGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLN 819 G+G+RE S+ P Q+ +K V H D + RL ++L+ Sbjct: 540 GMGLREFSMHPSQLLRVKQEVLHADCERLERLVEQVLS 577 Lambda K H 0.319 0.134 0.386 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: 1023 Number of extensions: 43 Number of successful extensions: 4 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: 837 Length of database: 591 Length adjustment: 39 Effective length of query: 798 Effective length of database: 552 Effective search space: 440496 Effective search space used: 440496 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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