Align Dicarboxylate (succinate, fumarate, malate) transporter, vcINDY (characterized)
to candidate WP_011372775.1 SUDEN_RS06000 sodium:sulfate symporter
Query= TCDB::Q9KNE0 (462 letters) >NCBI__GCF_000012965.1:WP_011372775.1 Length = 482 Score = 174 bits (440), Expect = 8e-48 Identities = 136/449 (30%), Positives = 224/449 (49%), Gaps = 53/449 (11%) Query: 31 LFLALYHFLP---FEHNVVLGISMLAFIAVLWLTEALHVTVTAILVPVMAVFFGIF---- 83 LF FLP V + +L F A LW +EA+ ++LV + + F Sbjct: 32 LFAYFVAFLPTYQLSQKGVFTLFILLFAAALWASEAIPAFAVSLLVIALEIILLGFDDFN 91 Query: 84 ------ETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFM 137 E Q L +++ +IFLFL GF +A A LD A +VL A + + Sbjct: 92 FSSNSKEWQYYLEPWSSPLIFLFLAGFIMAEAASKTKLDLWFAKRVLFFAGEEPKNIITA 151 Query: 138 LFGVTALLSMWISNTATAAMML----PLVLGVLSKVDADKQRSTYVFVLLGVAYSASIGG 193 + +T +LSM++SNTATAAMM+ PL+L + S K +LL V A+IGG Sbjct: 152 IMSITFILSMFVSNTATAAMMMSVLSPLLLSIKSNNPLRKA------LLLSVVIGANIGG 205 Query: 194 IATLVGSPPNAIAAA---EVGLSFTDWMKFGLPTAMMMLPMAIAILYFLLKPTLNGMFEL 250 +AT++G+PPNAIA + SF +W+ +P A+MM+ + +L P+ L Sbjct: 206 MATIIGTPPNAIAVGMLKDNAPSFMEWIIIAMPPAVMMV-FLMRLLIIKFYPSNQTYINL 264 Query: 251 DRAP-VNWDKG--------------KVVTLGIFGLTVFLWIFSSPINAALGGFKSFDTLV 295 D + D G K + + IF +T+ LW+ S+ + T+V Sbjct: 265 DALDGIEDDDGTAKESAKDLLPSWKKQIVILIFFITISLWLTSALHHIP-------TTVV 317 Query: 296 ALGAILMLSFARVVHWKEIQKTADWGVLLLFGGGLCLSNVLKQTGTSVFLANALSDMVSH 355 +L I+ + ++ +I ++ W V++L GGL L + + G V+ A+ +S Sbjct: 318 SLLPIVAFTLFGIIDADDI-RSIRWDVIILIIGGLSLGLGVSKYGLDVWFASLISS--DG 374 Query: 356 MGIFVVILVVATFVVFLTEFASNTASAALLIP-VFATVAEAFGMSPVLLSVLIAVAASCA 414 + + +V+ V + VV ++ F SNTA+ +++P V A V S + ++ +A++AS A Sbjct: 375 LSVLMVLGVFSYIVVVISNFMSNTAATNIMLPIVIAIVTTLSSDSSQIAAIAVALSASFA 434 Query: 415 FMLPVATPPNAIVFASGHIKQSEMMRVGL 443 LPV+TPPNAI++ASG +K + + +G+ Sbjct: 435 MSLPVSTPPNAIIYASGIVKSKDFLFIGV 463 Score = 74.7 bits (182), Expect = 6e-18 Identities = 53/184 (28%), Positives = 95/184 (51%), Gaps = 13/184 (7%) Query: 49 ISMLAFIAV-LWLTEALH---VTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGF 104 + ++ FI + LWLT ALH TV ++L V FGI + + + +I L +GG Sbjct: 293 VILIFFITISLWLTSALHHIPTTVVSLLPIVAFTLFGIIDADD-IRSIRWDVIILIIGGL 351 Query: 105 ALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFG-VTALLSMWISNTATAAMMLPLVL 163 +L + GLD A L + G + V +F + ++S ++SNTA +MLP+V+ Sbjct: 352 SLGLGVSKYGLDVWFAS--LISSDGLSVLMVLGVFSYIVVVISNFMSNTAATNIMLPIVI 409 Query: 164 GVLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVGSPPNAIAAAEVGLSFTDWMKFGLP 223 +++ + +D + + V L +++ S+ V +PPNAI A + D++ G+ Sbjct: 410 AIVTTLSSDSSQIAAIAVALSASFAMSLP-----VSTPPNAIIYASGIVKSKDFLFIGVV 464 Query: 224 TAMM 227 TA++ Sbjct: 465 TALI 468 Lambda K H 0.329 0.139 0.417 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: 582 Number of extensions: 41 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 462 Length of database: 482 Length adjustment: 33 Effective length of query: 429 Effective length of database: 449 Effective search space: 192621 Effective search space used: 192621 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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