Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate Pf6N2E2_1812 peptide ABC transporter, ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1812 Length = 338 Score = 193 bits (490), Expect = 1e-53 Identities = 117/329 (35%), Positives = 178/329 (54%), Gaps = 17/329 (5%) Query: 22 DGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLKDKDIL 81 D + V ++FEV E+ I GESGCGKS ++A+ LL + L D+L Sbjct: 22 DDMLHAVRGLDFEVERGEMLCIVGESGCGKSLTSLALMDLLPRKARRTASRLTLDGIDML 81 Query: 82 SITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHG-VNVEEARKLIKEKLE 140 ++ + LR + Q M +L+P IGDQ+ H V+ ++A + LE Sbjct: 82 GQSERRMCDLRGNRLAMIFQEPMTSLNPAYSIGDQLSEVLTQHRKVSRKDALARAAQMLE 141 Query: 141 LVDLPYNV--VNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILKDL 198 V + + YPH+LSGG+RQRV+IA +++ P LII DEPTT LDV +Q +IL+ + Sbjct: 142 KVGISNAAERLRQYPHQLSGGLRQRVIIAMALMCEPDLIIADEPTTALDVTIQAQILRLI 201 Query: 199 KRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLISS 258 + IQ++LG++++ I+HD+ ++ I+DRV +MYAGEIVE ++ + P HPYT L++S Sbjct: 202 RDIQKELGLAVIFITHDLGLVARIADRVAVMYAGEIVETAPARQLFENPQHPYTRGLLAS 261 Query: 259 --LPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPALGDIMDGHKA 316 +P K E L SIPG P ++ + C F +RC + C+ P + DGH A Sbjct: 262 IPIPGRTKPGEALGSIPGLVPSLVGE-QQGCAFRNRCAQAITACAQDIPEIE--QDGHMA 318 Query: 317 RCFLQKGGYVDLSTLPIPLEYYAEEKAET 345 RC L P P +E+A + Sbjct: 319 RC---------LFAAPAPAPIRLQERARS 338 Score = 164 bits (415), Expect = 6e-45 Identities = 91/245 (37%), Positives = 150/245 (61%), Gaps = 7/245 (2%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMI----QQTSGKIILLGKDVSEYG 433 ++AV + FE+++G + +VG SG GKS + L ++ ++T+ ++ L G D+ Sbjct: 25 LHAVRGLDFEVERGEMLCIVGESGCGKSLTSLALMDLLPRKARRTASRLTLDGIDMLGQS 84 Query: 434 VRNSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNV 492 R + N + MIFQ+P +SL+P +++ + L H+KVS KD L + ++L+ V Sbjct: 85 ERRMCDLRGNRLAMIFQEPMTSLNPAYSIGDQLSEVLTQHRKVSRKDALA-RAAQMLEKV 143 Query: 493 GLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKK 552 G+ + L +YPH+LSGG RQRV IA A EP +++ADEP + LD +++A IL LI+ Sbjct: 144 GISNAAERLRQYPHQLSGGLRQRVIIAMALMCEPDLIIADEPTTALDVTIQAQILRLIRD 203 Query: 553 FKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 +K G+++++ITHD+ V IAD + V+Y G IVE ++ NP H YT+ L+ ++P Sbjct: 204 IQKELGLAVIFITHDLGLVARIADRVAVMYAGEIVETAPARQLFENPQHPYTRGLLASIP 263 Query: 612 DPYKT 616 P +T Sbjct: 264 IPGRT 268 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: 447 Number of extensions: 18 Number of successful extensions: 6 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: 338 Length adjustment: 33 Effective length of query: 584 Effective length of database: 305 Effective search space: 178120 Effective search space used: 178120 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