Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate H281DRAFT_01032 H281DRAFT_01032 peptide/nickel transport system ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Burk376:H281DRAFT_01032 Length = 340 Score = 197 bits (501), Expect = 6e-55 Identities = 105/297 (35%), Positives = 174/297 (58%), Gaps = 5/297 (1%) Query: 28 VTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVV-LRGHVYLKDKDILSITQE 86 V V+F V+ E + GESGCGKS ++A+ GLL P + G + + D+ +++ Sbjct: 29 VDRVSFLVHAGETLCVVGESGCGKSVTSLALMGLLASPPARRVAGTAHFEGVDLFGLSER 88 Query: 87 ELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GVNVEEARKLIKEKLELVDLP 145 EL +R + Q M +L+P +G+Q+ + H GV+ AR+ + L LV +P Sbjct: 89 ELADIRGNRMSMIFQEPMTSLNPAYTVGEQIGESIRRHRGVSRAAAREEALKMLRLVHIP 148 Query: 146 YNVVNM--YPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILKDLKRIQR 203 + + H+LSGGMRQRV+IA ++ +P L+I DEPTT LDV +Q ++L ++ +Q+ Sbjct: 149 APETRLDAFAHQLSGGMRQRVMIAMALANSPRLLIADEPTTALDVTIQAQVLALVRNLQK 208 Query: 204 QLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLISSLPSLV 263 + G ++++I+HD+ ++ ++D V +MYAG+IVE G+ ++ P HPYT L+ ++PS+ Sbjct: 209 ETGTAMLLITHDLGVVAEVADHVAVMYAGKIVEYGTVSDLFDDPQHPYTIGLMGAIPSVG 268 Query: 264 KRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPALGDIMDGHKARCFL 320 KR L +I G+ P ++P CRF RCPF ++C P + H+ C+L Sbjct: 269 KREGSLATIRGSVPTP-EQMPRGCRFAPRCPFAEQRCIDAAPPERTLEGEHRVACWL 324 Score = 142 bits (357), Expect = 3e-38 Identities = 87/245 (35%), Positives = 139/245 (56%), Gaps = 8/245 (3%) Query: 374 LSEPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMI-----QQTSGKIILLGKD 428 L + N V+ VSF + G +VG SG GKS + L G++ ++ +G G D Sbjct: 22 LPDAPNVVDRVSFLVHAGETLCVVGESGCGKSVTSLALMGLLASPPARRVAGTAHFEGVD 81 Query: 429 VSEYGVRNSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIE 487 + R + N + MIFQ+P +SL+P +TV + + H+ VS + + ++ Sbjct: 82 LFGLSERELADIRGNRMSMIFQEPMTSLNPAYTVGEQIGESIRRHRGVS-RAAAREEALK 140 Query: 488 VLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGIL 547 +L+ V + PE L + H+LSGG RQRV IA A A P++L+ADEP + LD +++A +L Sbjct: 141 MLRLVHIPAPETRLDAFAHQLSGGMRQRVMIAMALANSPRLLIADEPTTALDVTIQAQVL 200 Query: 548 NLIKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRL 606 L++ K+ G ++L ITHD+ V +AD + V+Y G+IVE G ++ +P H YT L Sbjct: 201 ALVRNLQKETGTAMLLITHDLGVVAEVADHVAVMYAGKIVEYGTVSDLFDDPQHPYTIGL 260 Query: 607 IEAVP 611 + A+P Sbjct: 261 MGAIP 265 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: 415 Number of extensions: 25 Number of successful extensions: 8 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: 340 Length adjustment: 33 Effective length of query: 584 Effective length of database: 307 Effective search space: 179288 Effective search space used: 179288 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