Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Cola:Echvi_3627 Length = 431 Score = 368 bits (944), Expect = e-106 Identities = 192/423 (45%), Positives = 289/423 (68%), Gaps = 5/423 (1%) Query: 5 ILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMI---QVASGVNKFSLLAIPFF 61 IL+ SFI L+ +G+PVA++LG S+L+ + +M ++ +G+N FSLLAIPFF Sbjct: 8 ILVLSFITLMGLGVPVAWSLGFSSLLTLMVTVAAVPSMTTIAQRMGAGLNSFSLLAIPFF 67 Query: 62 VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121 +LAG IM +GG++ RL+ A L G + GGL VN++A+ FGAI+GS+VA +++G +L Sbjct: 68 ILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASALGGIL 127 Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181 ME +GYP+E AV V+ S L+ PPS+ ++YSLA+GG VSIA+LF+AG +PGL Sbjct: 128 GKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGG-VSIAALFVAGYIPGLF 186 Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241 + ++M F KK+ P GE +E K+ A L +VI++GGI+ GVFTATE+ Sbjct: 187 MGLLLMLTAAYFIKKKKLPAGEPTSFKELGKVFFSAAPSLTLLVIVIGGIVMGVFTATEA 246 Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301 +A+AV++ ++ F Y + K RDLP ++ ++ T ++V +LI + + +VM+ IP Sbjct: 247 SAIAVLYCLGLSFF-YGELKPRDLPAILLKSSATTAVVAMLIATSMAMSWVMSSEDIPQS 305 Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361 I+ L+LSDN++VIL+ IN +L+ +G MDM P +LI TPI LPV+T +G+DPVHFG+I Sbjct: 306 ISAVLLSLSDNKFVILIIINLILLFVGIFMDMTPAVLIFTPIFLPVVTELGIDPVHFGII 365 Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWL 421 M++NL IGL TPPVG+VLF+G + K SI + VK L+PF++A+ + L +T P ++LWL Sbjct: 366 MVLNLCIGLCTPPVGSVLFIGVGVAKTSISNVVKPLLPFFIAMIIGLAVITIWPQLTLWL 425 Query: 422 PSV 424 PS+ Sbjct: 426 PSL 428 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: 573 Number of extensions: 34 Number of successful extensions: 6 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: 431 Length adjustment: 32 Effective length of query: 394 Effective length of database: 399 Effective search space: 157206 Effective search space used: 157206 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