Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate H281DRAFT_04094 H281DRAFT_04094 peptide/nickel transport system ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Burk376:H281DRAFT_04094 Length = 744 Score = 337 bits (865), Expect = 8e-97 Identities = 213/595 (35%), Positives = 340/595 (57%), Gaps = 31/595 (5%) Query: 30 NVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLKDKDILSITQEELR 89 +V+F V E + + GESGCGKST+AMA L G V G + + D+ + + LR Sbjct: 44 DVSFRVRRGEAYGLVGESGCGKSTVAMAALRYLPRNGKVKAGKIVIAGADVNKLDADALR 103 Query: 90 KLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHGVNVEEARKLIKEKLELVDL--PYN 147 +R V Q AL+P I Q+ A + GV +EA + E L+ V + P Sbjct: 104 TMRANTISMVYQDPARALNPSLTIARQVSEAFEAAGVAPDEALQRSLEMLQRVRIASPER 163 Query: 148 VVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILKDLKRIQRQLGV 207 V++ YPH+LSGGM+QRVVIA ++ NP+L+ILDEPTTGLD V+ E+L + +++ +LG Sbjct: 164 VMDSYPHQLSGGMQQRVVIAMALASNPALLILDEPTTGLDATVEAEVLDLVAQLRAELGT 223 Query: 208 SLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLISSLPSL--VKR 265 +++ ISH+++++ + +RVG++YAG++VE G+ +++ RP HPYT L+ LP++ K Sbjct: 224 AVLFISHNLAVIGRMCERVGVLYAGKLVEEGATQDVFTRPRHPYTVGLLRCLPTVGRSKD 283 Query: 266 REKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPALGDIMDGH---KARCFLQK 322 E+L +I G P V C + +RC ++C P + H +RC + Sbjct: 284 TERLDTIAGGLP-SPGSVTQGCIYAERCRLADDRCRREAPPPYRVSAAHGDQMSRCHYHE 342 Query: 323 GGYVDLSTLPIPLEYYAEEKAETDL--SESNQHEVVMKILNLSKIYYIRKNLILSEPINA 380 LP L A+ E DL ++ N E+V++ NLSK +++ + A Sbjct: 343 RAI----ELPRAL---AQALPEHDLANADKNPRELVLRAENLSKTFHVS-----GTALRA 390 Query: 381 VNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTSGKIILL-GKDVSEYGVRNSMW 439 V+ VS +L G LVG SG GK+T+AK++ G++ +G ++ L G ++ R + Sbjct: 391 VDKVSLDLAAGETLGLVGESGSGKTTLAKLMLGLLAPDAGSVLELDGAPLAARVTRRNDE 450 Query: 440 YKENVQMIFQDPYSSLDPRHTVRWHVERPL--LIHKKVSNKDQLLPKIIEVLKNVGLKPP 497 +++Q++FQ+P S+L+ H+V+ + R L L + + D+ L + ++ P Sbjct: 451 QVKSLQIVFQNPDSALNRAHSVKRLIGRALSRLAALRGAAIDERLATL-----TAAVRLP 505 Query: 498 EKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKKF-KKN 556 E+YL +LSGG +QRVAIARA A EP+V+V DEP S LD S++A ILNL+ ++ Sbjct: 506 ERYLGSRTRQLSGGLKQRVAIARAFAGEPRVVVCDEPTSALDVSVQAAILNLLADLQRER 565 Query: 557 GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 G+S ++I+HD+ V Y++D I V+Y GR++E G V P H YT+ L+ +VP Sbjct: 566 GVSYVFISHDLHVVRYLSDRIAVLYLGRLLEIGPAAAVFDGPQHPYTEALLSSVP 620 Score = 150 bits (379), Expect = 2e-40 Identities = 87/272 (31%), Positives = 154/272 (56%), Gaps = 14/272 (5%) Query: 346 DLSESNQHEVVMKILNLSKIYYIRKNLILSEPINAVNDVSFELKKGTITALVGGSGHGKS 405 D+S+S++ + + ++ L+ Y +R + DVSF +++G LVG SG GKS Sbjct: 13 DVSKSDRTDA-LTVVGLTVTYRMR-----GRDREVLQDVSFRVRRGEAYGLVGESGCGKS 66 Query: 406 TIAKILAGMIQQT----SGKIILLGKDVSEYGVRNSMWYKEN-VQMIFQDPYSSLDPRHT 460 T+A + + +GKI++ G DV++ + N + M++QDP +L+P T Sbjct: 67 TVAMAALRYLPRNGKVKAGKIVIAGADVNKLDADALRTMRANTISMVYQDPARALNPSLT 126 Query: 461 VRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIAR 520 + V D+ L + +E+L+ V + PE+ + YPH+LSGG +QRV IA Sbjct: 127 IARQVSE--AFEAAGVAPDEALQRSLEMLQRVRIASPERVMDSYPHQLSGGMQQRVVIAM 184 Query: 521 ATAVEPKVLVADEPVSMLDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMV 579 A A P +L+ DEP + LDA++ A +L+L+ + + G ++L+I+H++A + + + + V Sbjct: 185 ALASNPALLILDEPTTGLDATVEAEVLDLVAQLRAELGTAVLFISHNLAVIGRMCERVGV 244 Query: 580 IYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 +Y G++VE+G T +V + P H YT L+ +P Sbjct: 245 LYAGKLVEEGATQDVFTRPRHPYTVGLLRCLP 276 Score = 140 bits (353), Expect = 2e-37 Identities = 98/311 (31%), Positives = 156/311 (50%), Gaps = 14/311 (4%) Query: 8 LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67 +L+ L+ + + V V+ ++ E + GESG GK+TLA + GLL Sbjct: 371 VLRAENLSKTFHVSGTALRAVDKVSLDLAAGETLGLVGESGSGKTTLAKLMLGLLAPDA- 429 Query: 68 VLRGHVYLKDKDILS--ITQEELRKLRMKEFVYV-PQFAMDALDPVAK-IGDQMMRAAVS 123 G V D L+ +T+ +++ + V+ P A++ V + IG + R A Sbjct: 430 ---GSVLELDGAPLAARVTRRNDEQVKSLQIVFQNPDSALNRAHSVKRLIGRALSRLAAL 486 Query: 124 HGVNVEEARKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPT 183 G ++E + V LP + +LSGG++QRV IA + P +++ DEPT Sbjct: 487 RGAAIDERLATLTAA---VRLPERYLGSRTRQLSGGLKQRVAIARAFAGEPRVVVCDEPT 543 Query: 184 TGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEI 243 + LDV VQ IL L +QR+ GVS V ISHD+ ++ +SDR+ ++Y G ++EIG + Sbjct: 544 SALDVSVQAAILNLLADLQRERGVSYVFISHDLHVVRYLSDRIAVLYLGRLLEIGPAAAV 603 Query: 244 IKRPSHPYTYLLISSLPSLVKRRE-KLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK-CS 301 P HPYT L+SS+P+L + + G+ P S P+ C F+ RCP K+ C Sbjct: 604 FDGPQHPYTEALLSSVPTLDGHASVARVRLSGDLPSAASP-PSGCVFHTRCPRKLGAICE 662 Query: 302 TLNPALGDIMD 312 +P + D Sbjct: 663 QQDPPFAEAAD 673 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: 981 Number of extensions: 52 Number of successful extensions: 13 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 617 Length of database: 744 Length adjustment: 39 Effective length of query: 578 Effective length of database: 705 Effective search space: 407490 Effective search space used: 407490 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: 54 (25.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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