Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 1937061 b3578 predicted transporter (NCBI)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Keio:1937061 Length = 425 Score = 293 bits (749), Expect = 9e-84 Identities = 153/416 (36%), Positives = 251/416 (60%), Gaps = 3/416 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDI-PLQAMMIQVASGVNKFSLLAIP 59 M I LG + I IG+P+A+AL L +W+D+ +Q M + +G + FSLLAIP Sbjct: 1 MAVLIFLGCLLGGIAIGLPIAWALLLCGAALMFWLDMFDVQIMAQTLVNGADSFSLLAIP 60 Query: 60 FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119 FFVLAG IM GG+S+R+V LVG GGL V ++A+ ++SGS+VADTA+V + Sbjct: 61 FFVLAGEIMNAGGLSKRIVDLPMKLVGHKPGGLGYVGVLAAMIMASLSGSAVADTAAVAA 120 Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179 +L+P M YP + + SG + A + PPS +++ +++G +SI+ LFMAGI PG Sbjct: 121 LLVPMMRSANYPVNRAAGLIASGGIIAPIIPPSIPFIIFGVSSG--LSISKLFMAGIAPG 178 Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239 +++ A +M A + N P+ + ++E +W L VII+GG SG+FT T Sbjct: 179 MMMGATLMLTWWWQASRLNLPRQQKATMQEIWHSFVSGIWALFLPVIIIGGFRSGLFTPT 238 Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299 E+ AVA ++ FV IYR+ + L ++ +T S+VM L+ A +++T+ ++P Sbjct: 239 EAGAVAAFYALFVATVIYREMTFATLWHVLIGAAKTTSVVMFLVASAQVSAWLITIAELP 298 Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359 ++ L D+ ++ + I ++++G VMD+ P +LILTP+L+P++ G+DP++FG Sbjct: 299 MMVSDLLQPLVDSPRLLFIVIMVAILIVGMVMDLTPTVLILTPVLMPLVKEAGIDPIYFG 358 Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIP 415 ++ ++N IGLITPP+G VL V S + K+ + V+ + P+ L L+ +L+ +IP Sbjct: 359 VMFIINCSIGLITPPIGNVLNVISGVAKLKFDDAVRGVFPYVLVLYSLLVVFVFIP 414 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: 583 Number of extensions: 37 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: 425 Length adjustment: 32 Effective length of query: 394 Effective length of database: 393 Effective search space: 154842 Effective search space used: 154842 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