Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate WP_073041176.1 BUB04_RS15590 C4-dicarboxylate ABC transporter
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_900129305.1:WP_073041176.1 Length = 440 Score = 495 bits (1274), Expect = e-144 Identities = 246/440 (55%), Positives = 329/440 (74%), Gaps = 12/440 (2%) Query: 6 EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMAN 65 E L +MF +LL G+PVAF+L G A+ FGL+G G F+ +P RI+G+M N Sbjct: 3 ESLPGIMFLVLTILLMFGFPVAFTLLGTALCFGLIGFGWDFFN-----LLPLRIWGVMTN 57 Query: 66 YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125 +TLLA+P F+FMG MLE+SGIAE LLETM +L GR+RGGLA++VV+VGALL A+TG+V A Sbjct: 58 FTLLAVPLFVFMGVMLERSGIAEELLETMALLFGRMRGGLAISVVVVGALLGASTGIVGA 117 Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIG 185 TVV MGL+SLP MLR GY ELATG I+ASGTLGQIIPPS+VLV+LGD +G+SVGDLFIG Sbjct: 118 TVVTMGLLSLPTMLRRGYQPELATGTISASGTLGQIIPPSIVLVLLGDIIGVSVGDLFIG 177 Query: 186 SVIPGLMMASAFALHVLIVAFIRPDVAPALPA----QVREIGGKALGKRVIQVMIPPLIL 241 +VIPGL++ + +++ ++A I+P AP +P Q+ E G L +RV++ ++PPL L Sbjct: 178 AVIPGLVLVVLYIIYITVIARIKPKWAPLIPREEWDQILEAG---LFRRVMRALVPPLFL 234 Query: 242 ILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILI 301 ++ VLGSIF G A+PTEA AVG G++ LAAAN +F +E L QV TT R+T MV IL+ Sbjct: 235 MVSVLGSIFAGIASPTEAAAVGATGSMVLAAANKRFNMEILAQVMQTTTRLTCMVFIILV 294 Query: 302 GSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLF 361 G+ AF LVFRGL GD ++ + ++P GK G LF+ MT VF++GFF+DF EI FI IP+ Sbjct: 295 GAGAFGLVFRGLGGDHWVRSYIEHIPYGKWGVLFICMTIVFVIGFFLDFIEITFIHIPVL 354 Query: 362 VPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFIL 421 P+ + +G D +W+ ++ NLQTSF+TPPFGF+LFYL+GVAPPE+TT IYRG+IPF++ Sbjct: 355 APIMKDMGFDPLWFAILFAVNLQTSFMTPPFGFSLFYLKGVAPPEITTGHIYRGIIPFVI 414 Query: 422 LQLLVLLLIIIFPGIVSFLP 441 LQL+ LL ++ FP ++LP Sbjct: 415 LQLMGLLTLVFFPSFATWLP 434 Lambda K H 0.331 0.149 0.437 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: 636 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 440 Length adjustment: 32 Effective length of query: 413 Effective length of database: 408 Effective search space: 168504 Effective search space used: 168504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 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