Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate AO356_25640 AO356_25640 L-dehydroascorbate transporter large permease subunit
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25640 Length = 426 Score = 294 bits (752), Expect = 4e-84 Identities = 160/420 (38%), Positives = 256/420 (60%), Gaps = 3/420 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDI-PLQAMMIQVASGVNKFSLLAIP 59 M I LGS I + +GMP+A+AL + ++ ++D+ Q + + +G + F L+A+P Sbjct: 1 MTLVIFLGSLIGSMALGMPIAFALLVVSVALMVYLDLFDAQIIAQNLLNGADSFPLMAVP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FF+LAG IM GG+S+R+V A LVG RGGL V I+AS ++SGS+VAD A++ + Sbjct: 61 FFMLAGEIMNVGGLSKRIVNIAMALVGHKRGGLGYVAIIASCLLASLSGSAVADAAALAA 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 +L+P M G+ R S + +GS+ A + PPS +++ +A+G VSI+ LF+AGI+PG Sbjct: 121 LLVPMMVLAGHNRGRSAGLIAAGSIIAPVIPPSIGFIVFGVASG--VSISKLFLAGIVPG 178 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 L+L A + ++ N E L+ + W + +II+ G+ G+FT T Sbjct: 179 LMLGASLAVAWWYISRSENVETPPKRSRAEVLRTLLDGSWAMGLPLIIILGLKFGIFTPT 238 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E+A VA V+S FV++ IYR+ K L +++ + +T S+VM+L+ A +++T+ +P Sbjct: 239 EAAVVAAVYSLFVSLVIYREMKVSQLYEVILSSAKTTSVVMLLVAAAMVSSWLVTIADLP 298 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 ++ DN+ V+L+ + +++L+GTVMDM P ILILTP+L+P + G+DPV+FG Sbjct: 299 GQLAELLAPFMDNQTVLLLVMMVLIILVGTVMDMTPTILILTPVLMPAVIQAGIDPVYFG 358 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 ++ L+N IGLITPPVG VL V + K+ E V+ + PF A F+VL + P + L Sbjct: 359 VLFLINTAIGLITPPVGTVLNVVCGVAKLDFEEIVRGVWPFMFAQFVVLFLLVLFPQLVL 418 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: 553 Number of extensions: 32 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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