Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate 7025568 Shewana3_2719 choline/carnitine/betaine transporter (RefSeq)
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__ANA3:7025568 Length = 658 Score = 433 bits (1114), Expect = e-126 Identities = 223/508 (43%), Positives = 317/508 (62%), Gaps = 25/508 (4%) Query: 41 IHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVL 100 I+ VF S I L V+ + + FF +++WL + W ++ +F+I + + Sbjct: 7 INPPVFYSSVFFITLMVMICAIWPTEANHFFKSMQSWLEAKAGWLYILGVAIFLIFIIFV 66 Query: 101 IVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIEN 160 +V+ G +++G A PDYSY W+AMLF+AGMGIGL+FFGV+EP+ H+ + Sbjct: 67 MVSRFGDIKLGPDHAVPDYSYKSWIAMLFSAGMGIGLMFFGVAEPVMHYLAP-------- 118 Query: 161 GVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMR 220 A ++ AA+ M T +HW +H W+IY ++AL LA F++ LPL R Sbjct: 119 ---------PDATPESLAAAKEAMKITFFHWGIHAWAIYGVVALSLAYFAYRHKLPLLPR 169 Query: 221 SIFYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFG-VPMTDTTQ 279 S YPL GER+ G +GH +D AV+ T+FG+ATSLG+G Q +GL++LF +P T Q Sbjct: 170 SALYPLIGERIHGPIGHCVDTFAVLGTMFGVATSLGFGVLQVNSGLSYLFEQLPNNTTVQ 229 Query: 280 VVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIAS 339 V LI+ IT LA +SV +GLD GVKRLSE+N+ LA +LL V+I+GPT+ +L F N S Sbjct: 230 VSLIIGITLLATLSVFSGLDKGVKRLSELNLGLALILLLIVLILGPTVMLLQAFVQNTGS 289 Query: 340 YITNI--PALSMPFEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICV 397 Y+++I ++ + ++ GWT YW WWISWSPFVG FIARVSRGR++REF++ + Sbjct: 290 YLSDIVNKTFNLYAYQHKEDWLGGWTLLYWGWWISWSPFVGTFIARVSRGRTIREFLVGI 349 Query: 398 ILIPSTVCVLWMTAFGGTAISQYVNDGY----EAVFNAELPLKLFAMLDVMPFAEITSVV 453 + +PS + LWMT FG +AI +N G EAV N +P+ LF + MPF + S + Sbjct: 350 LFVPSALTFLWMTVFGNSAIDAIMNQGATYLSEAV-NTNVPVALFVFFEHMPFPHLLSGI 408 Query: 454 GIILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQ 513 GI LVV FF+TSSDSGSLVID + +GG +AP QRVFW +G+VA L+L GGL A Q Sbjct: 409 GICLVVTFFVTSSDSGSLVIDNLTSGGDNNAPVWQRVFWALLQGVVASVLLLAGGLQALQ 468 Query: 514 AMAVTTGLPFTIVLLVATVSLIKGLMDE 541 A+ + +PF V+L+ + L K L D+ Sbjct: 469 TAAIASAMPFLCVMLLMCLGLYKALKDD 496 Lambda K H 0.327 0.141 0.435 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: 941 Number of extensions: 46 Number of successful extensions: 5 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: 553 Length of database: 658 Length adjustment: 37 Effective length of query: 516 Effective length of database: 621 Effective search space: 320436 Effective search space used: 320436 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