Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Dino:3606890 Length = 432 Score = 455 bits (1170), Expect = e-132 Identities = 230/440 (52%), Positives = 302/440 (68%), Gaps = 14/440 (3%) Query: 1 MSDT----SFVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAA 56 MSDT +FVRTE + P P PVS+VG + W+R NLF ++ LT+ WL Sbjct: 1 MSDTHASAAFVRTEEIPPSPPPVSEVGIVNWLRSNLFYSIPSSILTLLTAAFIYWLSSIL 60 Query: 57 APWLLHGVWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVT 116 PW+ +GVW+ANS+ +CR I+ A G C+AVI RW Q +FG YP ++YWR + Sbjct: 61 MPWMFNGVWDANSIRDCREIL-----DGAIGGCFAVIAERWPQLIFGNYPNEEYWRAVLA 115 Query: 117 FAGLFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTAL 176 F GLF+ALAPVLF LPRK++W T L+P A+WL+WGG W V L G + + F AL Sbjct: 116 FVGLFVALAPVLFFKLPRKMLWFTGLFPFIAYWLIWGGSAWVSVMALVGVVVGYVAFKAL 175 Query: 177 APK--LGVPVSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIG 234 + G V+A L LFW++ + AL S + L+LP+V+S GGF++ ++G Sbjct: 176 EERSFFGAIVAA---LFATLLFWIFISPLAVNALSSVVALSLPQVESRFIGGFMINFILG 232 Query: 235 VTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGT 294 + I +SLPLGI LALGRQS++ I+K + V IEF+RGVPLITLLF AS++L YFLPPGT Sbjct: 233 TSGIALSLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGT 292 Query: 295 NFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALK 354 +FDL+LRV+I++TLFA+AYIAE IRGGLAALPRGQYEA D+LGLDYWQ+ RLII+PQALK Sbjct: 293 SFDLVLRVIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIILPQALK 352 Query: 355 ISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLF 414 ISIP IV+ IGLFKDTTLV+ + +FD L I + S W G YWE F ++FF+F Sbjct: 353 ISIPSIVNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLGFAGVLFFVF 412 Query: 415 NFSMSRYSMYLERKLKRDHR 434 + +S+YS +LER+L +HR Sbjct: 413 CYGISQYSQWLERQLATEHR 432 Lambda K H 0.329 0.143 0.457 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: 723 Number of extensions: 37 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: 434 Length of database: 432 Length adjustment: 32 Effective length of query: 402 Effective length of database: 400 Effective search space: 160800 Effective search space used: 160800 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: 51 (24.3 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