Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_086508281.1 BZY95_RS01725 TRAP transporter permease DctM/Q
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_002151265.1:WP_086508281.1 Length = 653 Score = 386 bits (992), Expect = e-111 Identities = 227/581 (39%), Positives = 338/581 (58%), Gaps = 23/581 (3%) Query: 165 RERSVFSVP--DLVLIVCSLAVAAYFL-----VVYNTSMRMSTGTSFAPVGISFAAIAGT 217 R+R VP D+V I +AV+AY++ ++Y M T F +A Sbjct: 73 RQRDAKRVPWYDIVPIALGVAVSAYYVHHFDRIIYQLGYLMPTTLDL------FFGVAAI 126 Query: 218 ALIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQVY-TDAGILGP 276 L++E RR G+A I+ L+ LAY G +LPG G+ G + Y + G+ G Sbjct: 127 LLLLEACRRAIGLAFPILVLIALAYAAFGNHLPGVWGHGGYRWDDLVATFYMSPTGVYGS 186 Query: 277 TTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGT 336 SST I++FI+F A L ++ GD F+ + AA GR GGPAK + S + G I+G+ Sbjct: 187 LMRTSSTVIVIFIMFGALLVTTGGGDSFMRLSNAATGRMSGGPAKAATLCSAMFGSISGS 246 Query: 337 SAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYT 396 +A NV +TG TIPLMKK GYS + A A EA+ASTGGQI+PPIMGA AF+MA++ Y Sbjct: 247 TAANVATTGVFTIPLMKKNGYSPRFAAATEASASTGGQILPPIMGAAAFVMADVISTSYL 306 Query: 397 EIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQC-YLFVPIIILIV 455 I AA+IPA+L++ +++ V FEA + G+ + + E P LR + L +P+I+LI Sbjct: 307 NIISAALIPALLFYLAIWMSVHFEAKRLGLNPIPKSERPTLRQGLYNIETLVIPLIVLIT 366 Query: 456 ALFMGYSVIRAGTLATVSAAVV---SWLSPNKM--GLRHILQALEIASYMAIQIIVVCAA 510 L M Y+ A A +A + SW SP ++ + ALE + A I V+ + Sbjct: 367 LLVMRYTPTTAAVAAYFTAMALYLFSWRSPGTFVERVKSLPAALEAGAMTAAMIAVIIGS 426 Query: 511 AGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVV 570 +I VISLTG+G + S ++L V+ L+ L+ AM ++I+LGMG+PT AAY +AASVV Sbjct: 427 VAIIAAVISLTGLGLKVSSVILIVSGGDVLITLLLAMVVAIILGMGLPTVAAYMLAASVV 486 Query: 571 APGLVQLGIEPLTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAA 630 A ++ G+ L+AH F+ YFA++S +TPPVALA+Y I+G++ T++ + +I + Sbjct: 487 AAAFIEAGLPSLSAHLFILYFAILSGVTPPVALAAYIGGAIAGSHWFRTALTATKISLGG 546 Query: 631 FIVPFMFFYNGALLMEAGWFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAA 690 F++PFMF Y+ LL + +IA A+ + G+ L+ +G+F SW+ R LL+AA Sbjct: 547 FLIPFMFIYHPPLLGDGTGLQIALAVGSGVLGITALAASTIGYFLR-PCSWLERGLLLAA 605 Query: 691 ALLMIEGGLWTDLTGIAL--AVLAFVIQKQRKTRLATAGAL 729 AL++I G L TD GIAL AV A+ + R T A++ L Sbjct: 606 ALMLISGQLVTDALGIALIGAVWAWQYRLNRSTLGASSSPL 646 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: 1215 Number of extensions: 67 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 729 Length of database: 653 Length adjustment: 39 Effective length of query: 690 Effective length of database: 614 Effective search space: 423660 Effective search space used: 423660 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