Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate BPHYT_RS31200 BPHYT_RS31200 peptide ABC transporter substrate-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__BFirm:BPHYT_RS31200 Length = 325 Score = 226 bits (576), Expect = 1e-63 Identities = 126/319 (39%), Positives = 185/319 (57%), Gaps = 5/319 (1%) Query: 9 LKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVV 68 L V L +F G V + +F+V P EI + GESG GKS ++ GL+ PG + Sbjct: 6 LSVQNLRTHFFTGAGVAKAVDDTSFDVAPGEIVGLVGESGSGKSITGFSVLGLIDAPGRI 65 Query: 69 LRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHG-VN 127 + G V K +D+ ++T E LR+LR + Q M L+PV +I QM+ A +H V+ Sbjct: 66 VAGRVLFKGEDLTTLTPEALRRLRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVQAHTRVS 125 Query: 128 VEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTG 185 AR+ ++ L V +P + YPH+LSGGMRQRV IA ++L +P LII DEPTT Sbjct: 126 KHAARQRARDALASVGIPSPDERLRAYPHQLSGGMRQRVAIAIALLHDPELIIADEPTTA 185 Query: 186 LDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIK 245 LDV +Q +IL +++++ + ++V +SHD++++ ++DR+ +MYAG +VE GS +EI++ Sbjct: 186 LDVTIQAQILAEMQKLCARSHTAMVWVSHDLAVVAGLADRICVMYAGRVVETGSVDEILE 245 Query: 246 RPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNP 305 RP HPYT LI SLP +R E L IPG P L K+P C F RC + C + P Sbjct: 246 RPRHPYTIGLIDSLPEKARRGESLTQIPGMAPSAL-KLPVGCAFAPRCVYATSLCRSAEP 304 Query: 306 ALGDIMDGHKARCFLQKGG 324 + H RCF + G Sbjct: 305 PVTG-EGTHLFRCFHPRSG 322 Score = 149 bits (377), Expect = 1e-40 Identities = 86/239 (35%), Positives = 143/239 (59%), Gaps = 7/239 (2%) Query: 380 AVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEYGVR 435 AV+D SF++ G I LVG SG GKS + G+I +G+++ G+D++ Sbjct: 24 AVDDTSFDVAPGEIVGLVGESGSGKSITGFSVLGLIDAPGRIVAGRVLFKGEDLTTLTPE 83 Query: 436 NSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVGL 494 + N + MIFQDP +L+P + + + H +VS K + + L +VG+ Sbjct: 84 ALRRLRGNRIAMIFQDPMMTLNPVLRIDTQMIEAVQAHTRVS-KHAARQRARDALASVGI 142 Query: 495 KPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKKF- 553 P++ L YPH+LSGG RQRVAIA A +P++++ADEP + LD +++A IL ++K Sbjct: 143 PSPDERLRAYPHQLSGGMRQRVAIAIALLHDPELIIADEPTTALDVTIQAQILAEMQKLC 202 Query: 554 KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVPD 612 ++ ++++++HD+A V +AD I V+Y GR+VE G+ E++ P H YT LI+++P+ Sbjct: 203 ARSHTAMVWVSHDLAVVAGLADRICVMYAGRVVETGSVDEILERPRHPYTIGLIDSLPE 261 Lambda K H 0.319 0.138 0.391 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: 450 Number of extensions: 21 Number of successful extensions: 7 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: 617 Length of database: 325 Length adjustment: 32 Effective length of query: 585 Effective length of database: 293 Effective search space: 171405 Effective search space used: 171405 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 (21.7 bits) S2: 51 (24.3 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