Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q88NY5 (256 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 128 bits (321), Expect = 3e-34 Identities = 92/261 (35%), Positives = 148/261 (56%), Gaps = 19/261 (7%) Query: 13 MISIKNVNKWY----GDFQVLTD-------CSTEVKKGEVVVVCGPSGSGKSTLIKCVNA 61 ++ IKN+ WY G F TD + EV GE + + G SG GK+TL + + Sbjct: 309 LLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILR 368 Query: 62 LEPFQKGDIVVDGTSIAD-PKTNLPKLRSRVGMVFQ--HFELFPHLTITEN-LTIAQRKV 117 L G+I+ +G +I KT L KLR + ++FQ + L P L+I ++ L Q Sbjct: 369 LIQPTSGEIIFNGENITHIGKTALRKLRKDIQIIFQDPYASLNPKLSIGQSILEPLQVHK 428 Query: 118 LGRSEAEATKKGLALLDRVGLSA-HAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPT 176 L R+++E +K L LLD+VGL H ++P + SGGQ+QRV IARALA+ P ++ DE Sbjct: 429 LYRNDSERKQKVLELLDKVGLKEEHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESV 488 Query: 177 SALDPEMVSEVLDVMVQLAQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEF 235 SALD + ++VL+++ L E G+T + ++H++ + +++R++ M+KG I E+ E+ Sbjct: 489 SALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEEGFPEQI 548 Query: 236 FGDQSARDQRTQHLLSKILQH 256 F + + TQ L+ I H Sbjct: 549 F--YAPKAAYTQKLIEAIPGH 567 Score = 106 bits (265), Expect = 9e-28 Identities = 74/223 (33%), Positives = 124/223 (55%), Gaps = 12/223 (5%) Query: 26 FQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQK----GDIVVDGTSIADPK 81 F+ + S +VKKG V+ + G SGSGKS + L + G+I + S+ + Sbjct: 20 FKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLS 79 Query: 82 TN-LPKLR-SRVGMVFQHFELFPHLTITENLTIAQRKVLGRS--EAEATKKGLALLDRVG 137 +N + ++R +++ M+FQ + T +A+ +L R +AEA K +AL + V Sbjct: 80 SNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIALFNEVQ 139 Query: 138 LSAHAK---KHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMVQL 194 L K +P Q+SGGQ+QRV IA AL+ DP +++ DEPT+ALD + +L ++++L Sbjct: 140 LPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQLLLKL 199 Query: 195 AQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFF 236 QE M M+ ++H++G ++A+ V M KG I+E + F Sbjct: 200 KQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIF 242 Lambda K H 0.319 0.134 0.383 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: 324 Number of extensions: 22 Number of successful extensions: 9 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: 256 Length of database: 568 Length adjustment: 30 Effective length of query: 226 Effective length of database: 538 Effective search space: 121588 Effective search space used: 121588 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: 50 (23.9 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