Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_011840330.1 RSPH17029_RS02010 amino acid ABC transporter permease
Query= TCDB::Q52665 (434 letters) >NCBI__GCF_000015985.1:WP_011840330.1 Length = 442 Score = 568 bits (1463), Expect = e-166 Identities = 282/443 (63%), Positives = 338/443 (76%), Gaps = 10/443 (2%) Query: 1 MSDTS-----FVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQA 55 MSDT FVR ML P P ++ G + WMR+NLFSGPLN ALT+ GL+A ++++ Sbjct: 1 MSDTHAQTVPFVRETMLPPVAPPANEAGVVSWMRQNLFSGPLNIALTLLGLVAIYYVLEG 60 Query: 56 AAPWLLHGVWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFV 115 PWL+ VW A++L +CR II ERWG ATGACWAVIR RW QFL+GFYP YWR + Sbjct: 61 IVPWLMRSVWTADTLAQCRQIITERWGEGATGACWAVIRERWPQFLYGFYPNHLYWRPTL 120 Query: 116 TFAGLFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTA 175 TF LF+ALAP+LF +PR+++W +L YP AFWLLWGG I+ P+ AGF + G L Sbjct: 121 TFLLLFVALAPILFAQVPRQMLWFSLAYPFLAFWLLWGGSIFLPLVAAAGF-LFGWLAYR 179 Query: 176 LAPKLGVPVSAGIGLVVAALFWLYAAAPIEAALQS----ALPLALPEVDSDQFGGFLLAL 231 LA + G + +V L+WL+ A + L PL L EV SD+FGGF+LA+ Sbjct: 180 LAARFGTIAAVAAAALVPVLWWLFLAGDVSDDLARLTGRTFPLWLEEVRSDKFGGFVLAV 239 Query: 232 VIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLP 291 IGV+ I +SLPLGI+LALGR+SDM ++K+LSV IEF+RGVPLI LLFTASLLL YFLP Sbjct: 240 TIGVSGIALSLPLGIILALGRRSDMFLIKALSVSFIEFIRGVPLIALLFTASLLLNYFLP 299 Query: 292 PGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQ 351 PGT FD+ILRV+I+VTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYW+AQRLII+PQ Sbjct: 300 PGTTFDIILRVIIMVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWKAQRLIILPQ 359 Query: 352 ALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIF 411 ALKISIPGIVS+FIG+FKDTTLV FVGL DPLKGI++ VR+ WKG YWEPYIFV LIF Sbjct: 360 ALKISIPGIVSTFIGMFKDTTLVVFVGLLDPLKGITDAVRASTDWKGIYWEPYIFVGLIF 419 Query: 412 FLFNFSMSRYSMYLERKLKRDHR 434 F FNF+MSRYSM+LER+LK DHR Sbjct: 420 FAFNFAMSRYSMHLERRLKTDHR 442 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: 789 Number of extensions: 37 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: 434 Length of database: 442 Length adjustment: 32 Effective length of query: 402 Effective length of database: 410 Effective search space: 164820 Effective search space used: 164820 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 Apr 10 2024. 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