Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_084058008.1 B9A12_RS11345 C4-dicarboxylate ABC transporter permease
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_900176285.1:WP_084058008.1 Length = 601 Score = 379 bits (973), Expect = e-109 Identities = 215/593 (36%), Positives = 336/593 (56%), Gaps = 15/593 (2%) Query: 137 PVELEVWHFGWP--LLAATGVGIVMSWFHQRERSVFSVPDLVLIVCSLAVAAYFLVVYNT 194 PV + V H P ++ G G+ + R SV D++L + S+ Y++ + Sbjct: 6 PVSIPV-HVATPREMMWDCGNGLSYPFSKHSPRDRPSVFDVILALLSVLAVGYWVHQFEA 64 Query: 195 -SMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFL 253 + RM + T + ++ G L +E+ RRV G ++ ++GL+ Y + GPY+PG Sbjct: 65 LNYRMGSETQLD----FYVSVLGLLLSLEICRRVLGWSMTLVGLLAALYCYFGPYMPGPF 120 Query: 254 GYPGLSVQRFFSQVY-TDAGILGPTTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAA 312 + G ++R + ++ T G+ G +V TY+ILFI F AFL+ S G +F++F A A Sbjct: 121 AHRGFRLERIANHLFLTQDGVFGVMASVLVTYVILFIFFGAFLKKSGAGQFFLDFPMALA 180 Query: 313 GRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTG 372 GR+ GGPAKV+ AS G I+G++ N VSTG+ TIPLMKK G+ AGA+E +AS Sbjct: 181 GRTVGGPAKVACMASTFFGSISGSAIANTVSTGAFTIPLMKKAGFRPHVAGAIEPSASMV 240 Query: 373 GQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMRED 432 G MPPIMGAG F+MAE+T PY EI A+ PA+LYF SV+ MV FEA K + G+++D Sbjct: 241 GMFMPPIMGAGGFLMAELTRTPYVEIMKMAVGPALLYFLSVFTMVHFEAKKHNIVGVQDD 300 Query: 433 ELPKLRTMMKQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWLSP-NKMGLRHIL 491 L + K+ Y+ +P++I+IV + +GYS + AT+S VSW+ P N+MGLR I Sbjct: 301 IPRPLEILKKEWYMSIPLLIIIVLMLLGYSPGMSAFWATLSCIGVSWVRPENRMGLREIY 360 Query: 492 QALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISI 551 +A+ + + I G+IVG I+LTG+G +FS +++ ++ +A++ S+ Sbjct: 361 EAILDGARSTLVIGATVGVIGMIVGSIALTGIGLKFSDIIISLSGGHLAVAILLVGLASL 420 Query: 552 LLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPPVALASYAAAGI 611 +LGMG+P TAAY + A + P L ++G+ P+ AH V++F+ S ITPPV +A+YA A I Sbjct: 421 VLGMGVPVTAAYLITAVLAVPALDKMGVHPIAAHMIVYWFSQDSNITPPVCVAAYAGAAI 480 Query: 612 SGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTATFGVYMLSGGVL 671 +G++ +T SF+ ++ PF+F Y +L+ W EI A ++AT G S + Sbjct: 481 AGSDPWKTGWTSFKFAKFLYVGPFLFAYVPRILLMGTWQEIVMAYISATLGTLAFSAVTM 540 Query: 672 GWF--ASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQKQRKTR 722 G+ + WI + + +DL GIAL F Q+ + + Sbjct: 541 GYLLRKTTPVEWI---IFAMGTYMCYHPRFTSDLIGIALIACVFFWQRYKNKK 590 Lambda K H 0.327 0.139 0.410 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: 1074 Number of extensions: 65 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: 729 Length of database: 601 Length adjustment: 38 Effective length of query: 691 Effective length of database: 563 Effective search space: 389033 Effective search space used: 389033 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 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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