Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate WP_019894745.1 A377_RS0103375 hypothetical protein
Query= SwissProt::Q87NZ5 (553 letters) >NCBI__GCF_000384235.1:WP_019894745.1 Length = 708 Score = 399 bits (1024), Expect = e-115 Identities = 201/504 (39%), Positives = 307/504 (60%), Gaps = 26/504 (5%) Query: 45 VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104 VF + +VL +V TL+ + F+ + + +N WF++ + +F+I + ++P Sbjct: 25 VFIPAVSVLVLMIVGTLSNPELAGELFSATLSAITTNFGWFYMLAVALFLIFIFSVAISP 84 Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164 G++++G P+YS+ GW AMLF+AG GI L+FFGV+EP+ H++S Sbjct: 85 WGKIKLGPDHTEPEYSFGGWFAMLFSAGYGIALLFFGVAEPVLHYAS------------- 131 Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224 P GA DAA M +HW H W+IY L+ L LA F+F GLPL+MRS Y Sbjct: 132 ---PPNGAPETLDAAKQ-AMQIAFFHWGFHIWAIYGLVGLVLAYFAFRHGLPLSMRSTLY 187 Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLF-GVPMTDTTQVVLI 283 PL GER++G +GH +D A++ TVFGLAT+LG +Q GL++L +P+ + QVV + Sbjct: 188 PLIGERIYGPIGHTVDTFAILGTVFGLATTLGLSVAQINAGLHYLIPAIPVATSVQVVAL 247 Query: 284 VVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITN 343 VIT L + SVVAG++ G+KRLS IN+ LA L+ FV + GPT+ IL F N SY++ Sbjct: 248 GVITLLGIASVVAGMEKGIKRLSLINIGLAIALMAFVFLAGPTIFILEVFLQNTGSYLSG 307 Query: 344 IPALS---MPFEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILI 400 I + + R D + WT F + W I+W+PFVG+FIA++SRGR++R+F+ V+L+ Sbjct: 308 IVERTFNLQAYTRSD--WIGNWTLFIFGWTIAWAPFVGLFIAKISRGRTIRQFVFGVMLV 365 Query: 401 PSTVCVLWMTAFGGTAISQYVNDGYEAVFNA---ELPLKLFAMLDVMPFAEITSVVGIIL 457 P++ LW + FG TA+ +N+GY + + + LF + + +P E+ S + + L Sbjct: 366 PTSFTFLWFSVFGDTALHMIMNEGYSTLITQVQDDHAIALFKLFERLPLTEVISTITVFL 425 Query: 458 VVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAMAV 517 ++ FF+TSSDSGSLV+D++A+GG P QRVFW G++A L+L GGL A Q ++ Sbjct: 426 IITFFVTSSDSGSLVVDSLASGGAHYTPVWQRVFWAAMLGVIASVLLLAGGLKALQTASI 485 Query: 518 TTGLPFTIVLLVATVSLIKGLMDE 541 T LPF +++L+A V + + L E Sbjct: 486 TFALPFAVIMLIAAVGMWRALTIE 509 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: 951 Number of extensions: 49 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: 708 Length adjustment: 38 Effective length of query: 515 Effective length of database: 670 Effective search space: 345050 Effective search space used: 345050 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