Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate Ac3H11_3955 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3955 Length = 427 Score = 657 bits (1696), Expect = 0.0 Identities = 322/422 (76%), Positives = 379/422 (89%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60 M+ +LLG+F VL++IG+P+AY+LGLSAL GA WID+PL A+MIQVASGVNKFSLLAIPF Sbjct: 1 MDTLVLLGTFFVLMMIGVPIAYSLGLSALAGALWIDLPLDAVMIQVASGVNKFSLLAIPF 60 Query: 61 FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120 FVLAGAIMAEGGM+RRLVAFAGVLVGF+RGGLSLVNI+ASTFFGAISGSSVADTAS+GSV Sbjct: 61 FVLAGAIMAEGGMARRLVAFAGVLVGFIRGGLSLVNILASTFFGAISGSSVADTASIGSV 120 Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL 180 LIPEME+KGYPR F+TAVTVSGSVQA+L PPSHN+VLYSLAAGGTVSIA+LFMAG++PGL Sbjct: 121 LIPEMEKKGYPRPFATAVTVSGSVQAILIPPSHNAVLYSLAAGGTVSIAALFMAGVLPGL 180 Query: 181 LLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATE 240 L+ + LCL A + YPKGEVIPL++ALKI EALWGLM MVIILGGILSGVFTA E Sbjct: 181 LMGLTLAALCLFTAHREGYPKGEVIPLKQALKICVEALWGLMTMVIILGGILSGVFTANE 240 Query: 241 SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPS 300 SA++AVVW+FFVTMFIYRDYKWRDLPKL+HRTV+T+++VMILIGFAA+FGY+MT+M IP Sbjct: 241 SASIAVVWAFFVTMFIYRDYKWRDLPKLVHRTVKTVTVVMILIGFAAAFGYLMTMMMIPM 300 Query: 301 KITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGM 360 K+T +LSDN+YVIL IN ML+LLG +MDM+PLILILTPILLPV+ +GVDPVHFGM Sbjct: 301 KVTAFLTSLSDNKYVILAMINIMLLLLGCLMDMSPLILILTPILLPVVKMLGVDPVHFGM 360 Query: 361 IMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW 420 IM+VNLGIGLITPPVG VLF G+A+ K+ + +A+MPF++ALF+VL+ VTY+PAISLW Sbjct: 361 IMMVNLGIGLITPPVGTVLFTGAAVAKLPLGIVTRAMMPFFVALFVVLLMVTYVPAISLW 420 Query: 421 LP 422 LP Sbjct: 421 LP 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: 768 Number of extensions: 30 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: 426 Length of database: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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