Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate Ac3H11_552 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_552 Length = 384 Score = 194 bits (494), Expect = 3e-54 Identities = 127/367 (34%), Positives = 197/367 (53%), Gaps = 9/367 (2%) Query: 3 YKLSLLVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGV 61 +++S L AVA A AS + +A AGP++G A G+ + G+ A+ D+NA V Sbjct: 12 FRISALTAVALAASVASAQDVQTVKIAHAGPVSGGIAHIGKDTENGVRLAIDDLNAQNLV 71 Query: 62 LG-QKLKLEVG--DDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQ 118 +G +K+K E+ DDA DP+QA AVA +L V V GH SG+SIPAS +YA+ + Sbjct: 72 IGGKKIKFEIAAEDDAGDPRQATAVAQKLCDQKVAGVVGHLQSGTSIPASAIYAKCDLPH 131 Query: 119 ISPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLAD 178 I+ +++NP LT+ K FR+ D+ G + ++ K K+VAI+ D++AYG+G+A Sbjct: 132 ITASASNPDLTKPGHKTTFRLIANDNALGAALALFGADHQKLKSVAIIDDRTAYGQGVAS 191 Query: 179 ETQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQ 238 + G K E D+ A+++ +K + D ++ GG +AG + RQM+ Sbjct: 192 VFKATAQQKGLKVVAEEFTNDKATDFMAILTAIKNKKPDAIFYGGLDAQAGPMLRQMEQL 251 Query: 239 GL-NAPIVSGDALVTNEYWAITG--PAGEN-TMMTFGPDPREMPEAKEAVEKF-RKAGYE 293 GL N GDAL T + ++G PA +N T T G +M + +++ K + Sbjct: 252 GLGNVKYFGGDALCTEKLPELSGKTPALKNVTCATGGASVDKMQGGADWKKRYDAKFPGQ 311 Query: 294 PEGYTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYV 353 + Y+ Y Y A + A+A K+ANS D A L K Y V I F AKG++T+PA Sbjct: 312 FQIYSPYAYDAAMVLADAMKRANSVDPKVFAPFLAKTEYKGVTANIAFTAKGELTTPAVT 371 Query: 354 WYRWNNG 360 Y + +G Sbjct: 372 LYTFKDG 378 Lambda K H 0.312 0.129 0.366 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: 333 Number of extensions: 22 Number of successful extensions: 3 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: 366 Length of database: 384 Length adjustment: 30 Effective length of query: 336 Effective length of database: 354 Effective search space: 118944 Effective search space used: 118944 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 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