Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1 (characterized)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3040 (276 letters) >FitnessBrowser__Burk376:H281DRAFT_05890 Length = 317 Score = 177 bits (449), Expect = 3e-49 Identities = 97/288 (33%), Positives = 159/288 (55%), Gaps = 33/288 (11%) Query: 22 AILIFFPIFWMVLTSFKTEIDAFATPPQFIFMPTLENYLHI-----NERSDYFSF----- 71 A++ PI W+ LTSFKT+ DA A PP +F P++E Y+++ + ++ + Sbjct: 29 ALIAILPILWICLTSFKTQEDAIAYPPVVLFQPSMEGYVNLFTIRSRQTPEFIASLPPAQ 88 Query: 72 AW-----------------------NSVVISFSATALCLLIAVPAAYSMAFYETQRTRGT 108 W NS+VI F +T L + + AAY+ + ++ Sbjct: 89 TWYERDVRKRNMVIAGPSKVLPRFVNSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLADDL 148 Query: 109 LLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPR 168 L ++LST+M+PP+ V +PIYL+ ++ GL D+ + +IV+YT +N+ + VW++ + +IPR Sbjct: 149 LFFILSTRMMPPIAVAIPIYLMYRALGLSDSYVGMIVLYTAVNVSLAVWLLKGFMDEIPR 208 Query: 169 DILEAARLDGATLAQEMLRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTA 228 + EAA +DG T Q ++V+LP A G+A+T + LI WNE ++ LTS A + Sbjct: 209 EYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWNEYAFASLLTSGDAQTMPP 268 Query: 229 LIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 I G W ++A +TL PILIF + +K L+RG++FGAV+ Sbjct: 269 FIPFIIGEGGQDWPAVAAATTLFVVPILIFTVVLRKHLLRGITFGAVR 316 Score = 23.1 bits (48), Expect = 0.008 Identities = 8/23 (34%), Positives = 15/23 (65%) Query: 142 ALIVIYTLINLPIVVWMIYTYFK 164 A+++ Y LI + ++W+ T FK Sbjct: 23 AIVITYALIAILPILWICLTSFK 45 Lambda K H 0.328 0.138 0.427 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: 243 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 276 Length of database: 317 Length adjustment: 26 Effective length of query: 250 Effective length of database: 291 Effective search space: 72750 Effective search space used: 72750 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 (21.8 bits) S2: 48 (23.1 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