Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 6937828 Sama_1969 ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:D8IUD1 (522 letters) >FitnessBrowser__SB2B:6937828 Length = 301 Score = 89.4 bits (220), Expect = 2e-22 Identities = 74/234 (31%), Positives = 114/234 (48%), Gaps = 12/234 (5%) Query: 13 LLTLSGIGKRYAAPV-LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMML 71 L+ + KRY + LD + L + G +AL G NGAGK+TL ++CG + G + + Sbjct: 3 LIVTRNLTKRYGSKTALDDVSLQVEAGAPVALVGPNGAGKTTLMSLMCGYIQPDGGSLEI 62 Query: 72 DGQPYAPASRTQAEGLG-IRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAAR 130 G + P SR + LG + + Q+ L P S+ E L + F D ++ AE Sbjct: 63 LG--HVPGSR---QLLGKVCALPQDALLDPNFSVGEQLSFFASLQGFSAKDARREAERV- 116 Query: 131 AQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFS 190 +E+V L + P L G + V IA+ LIG+ + ++LDEPTA L + Sbjct: 117 --LELVELKDAARHKPTA-LSHGMGKRVAIAQALIGTPQLVLLDEPTAGLDPANARAVRE 173 Query: 191 RIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQL 244 I +E + SH LEEL+R+ D ++ L GKL + I S E+ + L Sbjct: 174 LISH-ASEQTTFLISSHNLEELERLCDTVLYLDKGKLSQSLSIKSESVERFLTL 226 Score = 57.8 bits (138), Expect = 5e-13 Identities = 59/244 (24%), Positives = 101/244 (41%), Gaps = 28/244 (11%) Query: 272 GRAPVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEIFI-----GDSQEP 326 G + SL + AG + + G G+G+T L+ L+ G + + G + I G Q Sbjct: 14 GSKTALDDVSLQVEAGAPVALVGPNGAGKTTLMSLMCGYIQPDGGSLEILGHVPGSRQLL 73 Query: 327 ARIRS-PKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGGMLDHAAESSVA 385 ++ + P+DA LL SV L+ S+ D E+ Sbjct: 74 GKVCALPQDA-----------------LLDPNFSVGEQLSFFASLQGFSAKDARREAERV 116 Query: 386 QDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEPTRGIDIGAKSDIY 445 + V+ + LS G ++V IA+ L ++L DEPT G+D A + Sbjct: 117 LELVEL----KDAARHKPTALSHGMGKRVAIAQALIGTPQLVLLDEPTAGLD-PANARAV 171 Query: 446 RLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADTFSRDDWSQERILAAAFSGY 505 R A++ L+ S +L EL ++CD + + G+++ + S S ER L + Sbjct: 172 RELISHASEQTTFLISSHNLEELERLCDTVLYLDKGKLSQSLSIKSESVERFLTLSLQDS 231 Query: 506 VGRQ 509 G + Sbjct: 232 AGEE 235 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: 349 Number of extensions: 17 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: 301 Length adjustment: 31 Effective length of query: 491 Effective length of database: 270 Effective search space: 132570 Effective search space used: 132570 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