Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate AZOBR_RS23930 AZOBR_RS23930 methionine ABC transporter ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__azobra:AZOBR_RS23930 Length = 329 Score = 201 bits (511), Expect = 4e-56 Identities = 125/319 (39%), Positives = 181/319 (56%), Gaps = 10/319 (3%) Query: 9 LKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVV 68 L++ +LT + DG V + V+ V A+ GESG GKS ++ GL+ PG V Sbjct: 1 LELRDLTTVFPGDDGPVTVIDGVSLAVRAGGTLAVVGESGSGKSMTFLSALGLVAAPGRV 60 Query: 69 LRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH---G 125 RG V + DIL E LR+LR + Q + AL+PV IG+Q++ +H G Sbjct: 61 RRGEVRIDGADILHQPPERLRRLRGAVISMIFQDPLTALNPVFTIGEQIVEVLRAHQRIG 120 Query: 126 VNVEEARKL-IKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184 AR + + ++++ D P V+ YPH+LSGG RQRV+IA +I L+P ++I DEPTT Sbjct: 121 RTAARARAIELLARVQIPD-PARRVDDYPHQLSGGQRQRVLIAMAIALSPKILIADEPTT 179 Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244 LDV VQ +IL L +Q + G++LV+I+HD+ ++ +D V +MYAG +VE GS EE+ Sbjct: 180 ALDVTVQAQILDLLADLQAETGMALVLITHDLGLVAKYADDVAVMYAGRLVETGSMEEVF 239 Query: 245 KRPSHPYTYLLISSLPSL-VKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK--CS 301 RP HPYT L S+P L E+L +I G PP ++++P C F RC + C Sbjct: 240 TRPRHPYTRALFRSIPRLDGPVDEELPAIEGQPP-NVARLPPGCAFEPRCTVGRGRADCC 298 Query: 302 TLNP-ALGDIMDGHKARCF 319 T P L GH++ CF Sbjct: 299 TRRPLPLAGDRSGHRSACF 317 Score = 149 bits (376), Expect = 2e-40 Identities = 84/241 (34%), Positives = 138/241 (57%), Gaps = 7/241 (2%) Query: 377 PINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTS----GKIILLGKDVSEY 432 P+ ++ VS ++ G A+VG SG GKS G++ G++ + G D+ Sbjct: 16 PVTVIDGVSLAVRAGGTLAVVGESGSGKSMTFLSALGLVAAPGRVRRGEVRIDGADILHQ 75 Query: 433 GVRNSMWYKENV-QMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKN 491 + V MIFQDP ++L+P T+ + L H+++ + + IE+L Sbjct: 76 PPERLRRLRGAVISMIFQDPLTALNPVFTIGEQIVEVLRAHQRIG-RTAARARAIELLAR 134 Query: 492 VGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIK 551 V + P + + YPH+LSGG+RQRV IA A A+ PK+L+ADEP + LD +++A IL+L+ Sbjct: 135 VQIPDPARRVDDYPHQLSGGQRQRVLIAMAIALSPKILIADEPTTALDVTVQAQILDLLA 194 Query: 552 KFK-KNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAV 610 + + G++++ ITHD+ V AD++ V+Y GR+VE G+ EV + P H YT+ L ++ Sbjct: 195 DLQAETGMALVLITHDLGLVAKYADDVAVMYAGRLVETGSMEEVFTRPRHPYTRALFRSI 254 Query: 611 P 611 P Sbjct: 255 P 255 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: 483 Number of extensions: 25 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: 329 Length adjustment: 33 Effective length of query: 584 Effective length of database: 296 Effective search space: 172864 Effective search space used: 172864 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