Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Pf1N1B4_2936 Putative sulfate permease
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2936 Length = 573 Score = 531 bits (1368), Expect = e-155 Identities = 289/548 (52%), Positives = 382/548 (69%), Gaps = 14/548 (2%) Query: 20 WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79 W+ Y+ R D+ AG+TVGIIAIPLAMALAI GVAPQ GLYT +A +IALTGGSR Sbjct: 16 WRAGYSLRRLRGDISAGVTVGIIAIPLAMALAIAVGVAPQQGLYTVLIAAPLIALTGGSR 75 Query: 80 FSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGF 139 F+VSGPTAAFVVIL P++QQ+GL GLL+ T+L+G LI +GL R GRLI+YIP VTLGF Sbjct: 76 FNVSGPTAAFVVILLPITQQYGLGGLLLCTMLAGAILIALGLIRAGRLIQYIPYPVTLGF 135 Query: 140 TSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFW 199 T+GIGI I T+Q+KD LGL EHY++++G L ALP+ +GD IG++ L +L+ W Sbjct: 136 TAGIGIVIATLQLKDLLGLSTTGHAEHYIEQLGGLLQALPSARLGDGIIGVMCLAVLIVW 195 Query: 200 PRLGIRLPGHLPALLAGCAVMGIVNLLGG-HVATIGSQFHYVLADGSQGNGIPQLLPQLV 258 PR R+PGHL AL G A++G+ GG VAT+G +F Y++ DG GIP LP Sbjct: 196 PRFVPRIPGHLVALAVG-ALLGVALESGGLAVATLGERFSYIV-DGVSHPGIPPFLPSFD 253 Query: 259 LPWDLP---NSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELV 315 PW+LP L++D IR L+ AF++AMLGAIESLLCAVV DGMTG+KH N+EL+ Sbjct: 254 WPWNLPGPYGQPLHLSYDLIRQLMAPAFAIAMLGAIESLLCAVVADGMTGSKHDPNAELL 313 Query: 316 GQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLP 375 GQGLGN++AP FGGITATAAIARSA NVR+GA SP++A+IHS +V+LA+L LAPL S+LP Sbjct: 314 GQGLGNLVAPLFGGITATAAIARSATNVRSGAFSPLAAIIHSAVVLLAILALAPLFSYLP 373 Query: 376 LSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLAS 435 ++A+AALL+MVAWNMSEA VV LR AP+ D++V+L C+SLTVLFDMV+A++VG++LA+ Sbjct: 374 MAALAALLVMVAWNMSEARHVVHTLRIAPRSDVLVLLTCLSLTVLFDMVLAVAVGLLLAA 433 Query: 436 LLFMRRIARMTRLAPV-------VVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKR 488 LF++R++ +T A + + D+P+ V + GPLFF AAE L + Sbjct: 434 GLFIKRMSDLTDTAELPREFHQALEDMPEHVRCYAIRGPLFFGAAEKALGVLRKFSPEVK 493 Query: 489 IVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGIQPIPGRLA 547 +VI++ AVP+LD L AF ++ +G L + + + RAGI +LA Sbjct: 494 VVIVEMSAVPMLDMTALAAFDNILRDYRTDGIGLILVGTAPRVRLKLRRAGIHREQRQLA 553 Query: 548 FFPNRRAA 555 + N A Sbjct: 554 YVNNLEQA 561 Lambda K H 0.328 0.142 0.425 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: 812 Number of extensions: 33 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: 559 Length of database: 573 Length adjustment: 36 Effective length of query: 523 Effective length of database: 537 Effective search space: 280851 Effective search space used: 280851 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: 53 (25.0 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