Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate PfGW456L13_2346 glutamine ABC transporter ATP-binding component
Query= uniprot:D8IUD1 (522 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2346 Length = 515 Score = 93.6 bits (231), Expect = 2e-23 Identities = 74/228 (32%), Positives = 118/228 (51%), Gaps = 13/228 (5%) Query: 8 SQGSPLLTLSGIGKRYAA-PVLDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASA 66 + +P+L L I K Y VL GIDL++ GQV+++ G +G+GK++L + + GL Sbjct: 255 NNATPILQLKNIQKSYGTHQVLMGIDLNVEYGQVVSIIGPSGSGKTSLIRTVNGLETIDT 314 Query: 67 GGMMLDGQPYAPAS------RTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWI 120 G ++L G+ + AS R + I MV Q NL P +I +N+ L PR G Sbjct: 315 GDILLFGEKFIEASDKPNSTRLRKGVRHIGMVFQNFNLFPHRTILDNVTLA--PRYHG-- 370 Query: 121 DRKKLAE-AARAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAM 179 +L+E A A ++ VGL P L G QQ V IAR L + ++ DEPT+ Sbjct: 371 QPGELSEHRAYALLDKVGLLAHAHKYP-HQLSGGQQQRVAIARALAMEPQIMLFDEPTSA 429 Query: 180 LTNREVELLFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKL 227 L V + + I L EG+ ++ ++H ++ I+DR+V + +G + Sbjct: 430 LDPELVNDVLNVIRDLAKEGMTMLIVTHEMDFAMSISDRVVFMENGNI 477 Score = 86.7 bits (213), Expect = 2e-21 Identities = 74/263 (28%), Positives = 123/263 (46%), Gaps = 23/263 (8%) Query: 264 PVLRIRGLGRAPVVHPA----SLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEIF 319 P+L+++ + ++ H L + G+V+ I G GSG+T L+R + G + + G+I Sbjct: 259 PILQLKNIQKSYGTHQVLMGIDLNVEYGQVVSIIGPSGSGKTSLIRTVNGLETIDTGDIL 318 Query: 320 I-GDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGGMLDH 378 + G+ A + ++ G+ + + L + I N +LA G + +H Sbjct: 319 LFGEKFIEASDKPNSTRLRKGVRHIGMVFQNFNLFPHRTILDNVTLAPRYHGQPGELSEH 378 Query: 379 AAESSVAQDYVKKLRIRSGSVAQA---AGELSGGNQQKVVIARWLYRDCPIMLFDEPTRG 435 A + L + G +A A +LSGG QQ+V IAR L + IMLFDEPT Sbjct: 379 RAYA---------LLDKVGLLAHAHKYPHQLSGGQQQRVAIARALAMEPQIMLFDEPTSA 429 Query: 436 IDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRI----ADTFSRDD 491 +D +D+ + +LA +G +L+V+ ++ M I DR+ M G I A R D Sbjct: 430 LDPELVNDVLNVIRDLAKEGMTMLIVTHEMDFAMSISDRVVFMENGNIQLDAAPETIRCD 489 Query: 492 WSQERILAAAFSGYVGRQEAAAA 514 ER+ F G R + +A Sbjct: 490 AEGERV--RRFMGISARSPSRSA 510 Lambda K H 0.320 0.137 0.390 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: 496 Number of extensions: 24 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: 2 Length of query: 522 Length of database: 515 Length adjustment: 35 Effective length of query: 487 Effective length of database: 480 Effective search space: 233760 Effective search space used: 233760 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: 52 (24.6 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