Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate BPHYT_RS02510 BPHYT_RS02510 C4-dicarboxylate ABC transporter
Query= TCDB::Q01857 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS02510 Length = 426 Score = 547 bits (1410), Expect = e-160 Identities = 272/415 (65%), Positives = 335/415 (80%) Query: 15 KKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGI 74 KKP + LYVQV+VAI GI LGHFYP L +KPLGD FIKL+KM+I P+IF TV TGI Sbjct: 2 KKPIHKVLYVQVIVAIIIGIALGHFYPNLAVDMKPLGDGFIKLIKMVIGPIIFCTVVTGI 61 Query: 75 AGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFA 134 AGM D++KVGRV GKA+LYF ST AL++GLI +V++PG G NIDPA+LD AVA++A Sbjct: 62 AGMEDMKKVGRVGGKALLYFEIVSTFALVLGLIATHVLKPGVGFNIDPATLDGKAVASYA 121 Query: 135 AKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNSL 194 AKAH Q+ V FL ++IP T+V AFA G+ILQ+L ++LFG LA GEKG+ V +F++ L Sbjct: 122 AKAHGQTTVDFLMHLIPDTLVSAFAQGEILQILLIALLFGAVLATAGEKGKVVTSFIDGL 181 Query: 195 TAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGAV 254 + +F +V I+ K APIGAFGAMAFTIGKYG+GS+ + LIGTFY+TS++FV +VLG + Sbjct: 182 SHVLFGIVRIITKLAPIGAFGAMAFTIGKYGIGSLLPMLKLIGTFYLTSIVFVVVVLGII 241 Query: 255 ARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSFN 314 AR GF+I+ + YIKEE+L+VLGTSSSEAALP LM K+EK GC RSVVGLV+PTGYSFN Sbjct: 242 ARAVGFNILRFVAYIKEEMLIVLGTSSSEAALPQLMLKLEKLGCSRSVVGLVVPTGYSFN 301 Query: 315 LDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVV 374 LDGTNIYMT+A LFIAQAT L+W Q+ LL V ML+SKGA+G+TGAGFITLAATL+VV Sbjct: 302 LDGTNIYMTMAVLFIAQATNTDLTWTQQLTLLAVTMLTSKGASGVTGAGFITLAATLAVV 361 Query: 375 PSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAAALGG 429 P++P++GM LILGIDRFMSECRALTN+VGN VAT+VV+ WE ELD +L AAL G Sbjct: 362 PTIPLSGMVLILGIDRFMSECRALTNIVGNGVATVVVSAWEKELDRNKLNAALRG 416 Lambda K H 0.324 0.139 0.393 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: 635 Number of extensions: 32 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 426 Length adjustment: 32 Effective length of query: 412 Effective length of database: 394 Effective search space: 162328 Effective search space used: 162328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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