Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AZOBR_RS32325 AZOBR_RS32325 PTS fructose transporter subunit IIA
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__azobra:AZOBR_RS32325 Length = 846 Score = 455 bits (1171), Expect = e-132 Identities = 293/672 (43%), Positives = 382/672 (56%), Gaps = 42/672 (6%) Query: 179 GLHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEA 238 GLHARPA + + A+ A I + A+AK+LVA++ L GD++ VSA G+DA A Sbjct: 179 GLHARPATAWVETARASAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVA 238 Query: 239 AIKALVALLAEGCGEAVVNVAEPVATQSSATLLRG------------VCASPGSAFGQV- 285 A+ + A + + A A Q + +RG + ASPG A G V Sbjct: 239 ALARMKATITRLTAREKADAA--AAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVH 296 Query: 286 ------VQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAA---GSAQAEIF 336 V V D + + E G E +LTR + L+ L D A G ++A IF Sbjct: 297 VLPRAAVSVPDEPVPLIEGGDR-LHEALSLTR------QNLKALADDTARRLGPSEAAIF 349 Query: 337 RAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVG 396 A E+L D L+ A +L+ EG A++W+ A T L N ++A RAADL DVG Sbjct: 350 AAQAEILNDTDLVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVG 409 Query: 397 QRVLKLILGI--QDSAWDLPER-AILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAI 453 QRVL I A DLP+ ILIAE L+PS TA+LD +V+G T GG TSH AI Sbjct: 410 QRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAI 469 Query: 454 LARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQR 513 LAR LGLPA+ A ++ LANG +LD G LHL P A+I A + R Sbjct: 470 LARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAE 529 Query: 514 DVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEE 573 + A+ LPA TRDGH VE+ ANV +V AL+ G E VGL+R+EFL+L+R AP +E Sbjct: 530 EEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDE 589 Query: 574 QAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLR 633 Q TY + AL R L+VR LD+GGDK + ++ + E NPFLG+RG RL L RP+LL Sbjct: 590 QYETYRGMLTAL-EGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLE 648 Query: 634 EQFRAILASA--GFAR----LHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMI 687 Q RA+ +A G A+ L IM PM++ L E+ R E L +P LGIM+ Sbjct: 649 TQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRAELDAPAVP-LGIMV 707 Query: 688 EVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVK 747 EVP+AA+ ADV A HVDFFSIGTNDLTQY LA+DR HP LA +ADS HPAVLRLI TV+ Sbjct: 708 EVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRLTVE 767 Query: 748 AAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIAR 807 A HG+WVGVCG +A + +L GLGV ELS++ IP +K +R DL+ + A+ Sbjct: 768 GAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQ 827 Query: 808 QVLGLEEAAEVR 819 + L E A VR Sbjct: 828 RALDCETADAVR 839 Lambda K H 0.318 0.133 0.371 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: 1517 Number of extensions: 72 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: 838 Length of database: 846 Length adjustment: 42 Effective length of query: 796 Effective length of database: 804 Effective search space: 639984 Effective search space used: 639984 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