Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate AZOBR_RS16500 AZOBR_RS16500 C4-dicarboxylate ABC transporter permease
Query= uniprot:E4PQE4 (729 letters) >FitnessBrowser__azobra:AZOBR_RS16500 Length = 673 Score = 383 bits (983), Expect = e-110 Identities = 213/533 (39%), Positives = 309/533 (57%), Gaps = 26/533 (4%) Query: 219 LIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQVY-TDAGILGPT 277 +++E TRR G L II L+F++Y GP +PG L +PG +V + +Y T G+ G Sbjct: 141 VLLEATRRSVGWPLPIISLIFMSYAIWGPQMPGLLKHPGATVSQLVDHLYLTTQGVYGIA 200 Query: 278 TAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTS 337 V +TY+ F++F F +G F++ A AGR GGPAKV+IF S L GMI+G+S Sbjct: 201 LGVVATYVFHFVLFGVFATRIGLGQLFLDCAAWVAGRYAGGPAKVAIFGSALFGMISGSS 260 Query: 338 AGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTE 397 N V+ GSLTIP MK++GY A AVE+ ASTGGQI PPIMGA AF+M E G+PYT Sbjct: 261 VANTVTVGSLTIPAMKRMGYKPHFAAAVESTASTGGQITPPIMGAAAFLMIEFLGLPYTT 320 Query: 398 IAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQCY-LFVPIIILIVA 456 I +AAI+PA ++F V V FEA + G+RG+R DE+P L+ ++ + +P+++LI Sbjct: 321 IIMAAIVPAFMHFFGVLVQVHFEAKRNGLRGLRPDEMPDLKEAFRRDWPTVIPLVVLIGI 380 Query: 457 LFMGYSVIRAGTLATVSAAVVSWLSPNK-MGLRHILQALEIASYMAIQIIVVCAAAGVIV 515 L GY+ A V L+P K M + +L L + A+ + A G+IV Sbjct: 381 LIAGYTPYMAAFWGITLCIAVGLLNPRKRMTIWEVLDGLRDGAKYALAVGAAAATVGIIV 440 Query: 516 GVISLTGVGARFSVL-------------------LLDVAATSQLLALIFAMFISILLGMG 556 GV++LTGVG + S + L D A + L LI + IL+G G Sbjct: 441 GVVTLTGVGFKISYIVTSTAGEMAVWAGAFLPGWLADAKALTLLFTLIMTGVVCILMGCG 500 Query: 557 MPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPPVALASYAAAGISGANA 616 +PTTA Y + A++ AP L LG+ P+ AHFFVFY+ V++ ITPPVALA+YAAAG++GA+ Sbjct: 501 IPTTANYIIMATIAAPALGLLGVAPIVAHFFVFYYGVLADITPPVALAAYAAAGMAGADP 560 Query: 617 METSVASFRIGIAAFIVPFMFFYNGALLMEA---GWFEIARALVTATFGVYMLSGGVLGW 673 +T +FR+G+A +VPF+F ++ +LL+ A W + A + G+ L + GW Sbjct: 561 FKTGNTAFRLGLAKALVPFVFVFSPSLLLVAPGFNWPDFFIAFLGCIVGIVCLGATLTGW 620 Query: 674 FASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQKQRKTRLATA 726 + W RLLL AA+L++ L++ L G+AL V + Q + + A Sbjct: 621 LLTNMRGW-ERLLLGIAAILLVTPELYSSLLGLALIVPVLLRQMSARRLMPEA 672 Score = 26.9 bits (58), Expect = 0.003 Identities = 15/44 (34%), Positives = 21/44 (47%) Query: 43 KFVALLAIAYSAFHLYSLNIAPLETWSFRIVHIAGALVLGFVLF 86 K V L I S FH Y+ L R +H++ L L F++F Sbjct: 30 KLVGGLLIILSLFHYYTAGFGLLPEMEHRGIHLSFVLGLVFLVF 73 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: 1273 Number of extensions: 83 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: 673 Length adjustment: 39 Effective length of query: 690 Effective length of database: 634 Effective search space: 437460 Effective search space used: 437460 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 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