Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-11560 (497 letters) >lcl|FitnessBrowser__SB2B:6938545 Sama_2648 aldehyde dehydrogenase (RefSeq) Length = 498 Score = 777 bits (2007), Expect = 0.0 Identities = 372/496 (75%), Positives = 435/496 (87%) Query: 2 TTLTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANR 61 T +R++WE AQ+L+I GRAFING Y DAV ETF+C+SPVDGR L +VASC ADA+ Sbjct: 3 TPQSRSEWEAMAQRLEINGRAFINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADI 62 Query: 62 AVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDI 121 AV NARA F SGVWS +P KRK +IRFA+LL + +ELALLETLDMGKPI S ++D+ Sbjct: 63 AVANARAVFESGVWSLQSPVKRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDV 122 Query: 122 PGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPA 181 GAA+AI W+ EAIDK+YDE+APTPH+++G++TREPVGVV AIVPWNFP+LMACWKLGPA Sbjct: 123 AGAARAIRWSGEAIDKIYDELAPTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPA 182 Query: 182 LATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLV 241 LATGNSVVLKPSEKSPLTAIR+AQLA EAG+P GVLNVLPG+GHTVG+ALALHMDVDTLV Sbjct: 183 LATGNSVVLKPSEKSPLTAIRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLV 242 Query: 242 FTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEV 301 FTGSTKIAKQLMVYAG+SNMKR+WLEAGGKSPNIVF DAPDL+AAAEAAASAIAFNQGEV Sbjct: 243 FTGSTKIAKQLMVYAGQSNMKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEV 302 Query: 302 CTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGH 361 CTAGSRLLVE +KD+ + ++V+ ++ W+PG+PLDP TT GA+VD QQ++TVL YI+AGH Sbjct: 303 CTAGSRLLVESGVKDELIKLIVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGH 362 Query: 362 KDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI 421 +GAKL+ GG + L ETGG YV PT+FDGVTN M+IA+EEIFGPV+SVI FD +EAVAI Sbjct: 363 DEGAKLMCGGSQVLAETGGVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAI 422 Query: 422 ANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSL 481 ANDT YGLAAG+WTSDISKAHKTA+A+R+G VW+N YDGGDMTAPFGG+KQSGNGRDKSL Sbjct: 423 ANDTIYGLAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSL 482 Query: 482 HALEKYTELKATWIKL 497 HA EKYTE+KATWI L Sbjct: 483 HAFEKYTEVKATWIAL 498 Lambda K H 0.316 0.132 0.390 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: 830 Number of extensions: 24 Number of successful extensions: 2 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: 497 Length of database: 498 Length adjustment: 34 Effective length of query: 463 Effective length of database: 464 Effective search space: 214832 Effective search space used: 214832 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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