Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 3609368 Dshi_2753 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Dino:3609368 Length = 429 Score = 326 bits (835), Expect = 1e-93 Identities = 176/418 (42%), Positives = 269/418 (64%), Gaps = 9/418 (2%) Query: 10 FIVLILIGMPVAYAL----GLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPFFVLAG 65 F++ ++IG+PV + L GL + DI L + V +G++ F L+AIPFF+LAG Sbjct: 9 FLLFLMIGLPVFFGLLAAPGLLLWLNGQERDITL--LYRNVYNGMDSFPLMAIPFFMLAG 66 Query: 66 AIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPEM 125 +M GG++ RLV FA L+G RGGL+ VNI++S F +SGS+VADT+++GS+LIP M Sbjct: 67 ELMNRGGITLRLVEFAQALMGHFRGGLAHVNILSSMLFAGLSGSAVADTSALGSMLIPAM 126 Query: 126 ERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSAV 185 E++GY R F+ A+T + SV + PPS ++Y+ G S+A+LF+AGI+PG+L+ Sbjct: 127 EKQGYTRRFAAAITAASSVIGPIIPPSGIMIIYAYVMGE--SVAALFLAGIVPGILVGVG 184 Query: 186 MMGLCLIFAKKRNYPKGEV-IPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAV 244 +MG+ + A K ++P + + + +A + LM VIILGGIL+GVFT TE+AAV Sbjct: 185 LMGVVKLMADKYDFPVASAKTTWGQRGQASLKAFFPLMTPVIILGGILAGVFTPTEAAAV 244 Query: 245 AVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKITT 304 AV ++ + F+ R K DLP ++ R T ++V++L+G A +F V++L P + Sbjct: 245 AVAYALIIGFFVMRTLKVSDLPDILGRAGITSAVVLLLVGAAMAFKTVVSLSYAPQIMAD 304 Query: 305 AFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIMLV 364 L+LS+N ++L+ IN +L ++G +D P I+IL PIL P+ +GVDP+HF +IM V Sbjct: 305 FMLSLSENPLILLLLINLLLFVVGMFLDAGPAIIILGPILGPIFVDLGVDPIHFAIIMSV 364 Query: 365 NLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWLP 422 NL +GL TPP+G VLFV S++ +E KA++PF LV+ +TY PAIS+ +P Sbjct: 365 NLTVGLATPPMGLVLFVASSVSGERVERIAKAILPFLAVEILVIFLITYFPAISMTIP 422 Lambda K H 0.329 0.142 0.418 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: 594 Number of extensions: 35 Number of successful extensions: 4 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: 426 Length of database: 429 Length adjustment: 32 Effective length of query: 394 Effective length of database: 397 Effective search space: 156418 Effective search space used: 156418 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 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