Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_086508594.1 BZY95_RS03465 C4-dicarboxylate ABC transporter
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_002151265.1:WP_086508594.1 Length = 638 Score = 400 bits (1029), Expect = e-116 Identities = 221/548 (40%), Positives = 334/548 (60%), Gaps = 9/548 (1%) Query: 171 SVPDLVLIVCSLAVAAYFLVVYNTSMRMSTG-TSFAPVGIS--FAAIAGTALIMELTRRV 227 S+ D +V S+ V AYF V S R++ T F P+ AA A L +E TRR Sbjct: 78 SLLDWCFVVASIIVGAYFFV---ESQRIAERITLFDPLETPDLLAASALLVLTIEATRRT 134 Query: 228 AGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFS-QVYTDAGILGPTTAVSSTYII 286 G L + LVF+AY G LPG G+ +S F ++T G+ G V++TY Sbjct: 135 VGFGLTSVVLVFVAYNLWGHSLPGAFGFREVSYNHFLDIMMFTSDGLFGVPLRVAATYAF 194 Query: 287 LFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGS 346 LF++F FL + ++F N + A AG GPAK+++ +SGL G ++G+ +VV+TGS Sbjct: 195 LFVMFGTFLSKAGGAEFFYNLSSAIAGSKPRGPAKIAVISSGLYGTMSGSPTSDVVTTGS 254 Query: 347 LTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPA 406 +TIP+M+++GYSK +G+VE AASTGG ++PP+MG+ AFIMAE TGI Y +I IA I+PA Sbjct: 255 VTIPIMQRLGYSKPLSGSVEVAASTGGSLLPPVMGSAAFIMAEYTGIEYRDIVIAGIVPA 314 Query: 407 ILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQCYLFV-PIIILIVALFMGYSVIR 465 +LYF VY V + K G++G+ +DE P L+ +K LF+ P++ L VAL MGYS Sbjct: 315 LLYFLCVYVQVHLRSQKLGLKGLPKDETPSLQETLKNGGLFILPLVALSVALVMGYSPTY 374 Query: 466 AGTLATVSAAVVSWLSPN-KMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVG 524 +ATVS VVS + P+ +M L+ I AL + + + ++ CAAAG+++G IS+TG+G Sbjct: 375 VAVIATVSVLVVSAVRPSTRMSLKAIWDALAVTTLRMVSVVAACAAAGLVIGGISMTGLG 434 Query: 525 ARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTA 584 +F+ L+ +A S ++AL+ + ++I+LGMGMPT +A+ +AA +V P L+ + + L A Sbjct: 435 GKFAELVFMLAGDSTVIALVISAMLAIILGMGMPTPSAFILAAVLVGPTLLSMDLSVLQA 494 Query: 585 HFFVFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALL 644 + F+ YFAV+SA+TPPVA+A++AA+ I+ A +E + + R+ I AFIVPF F + LL Sbjct: 495 NMFILYFAVLSAMTPPVAVAAFAASAIADAKPLEIATGAVRLAITAFIVPFAFVHGEGLL 554 Query: 645 MEAGWFEIARALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLT 704 + W +IA + ++A GV +LS V G++ R+ A LL I W + Sbjct: 555 LVGSWIDIAVSCISAVVGVLLLSVAVEGFWRQRLTKPFARVGFGVAGLLFIMPSWWAVVV 614 Query: 705 GIALAVLA 712 + LA Sbjct: 615 ALVCLTLA 622 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: 1138 Number of extensions: 73 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: 638 Length adjustment: 39 Effective length of query: 690 Effective length of database: 599 Effective search space: 413310 Effective search space used: 413310 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