Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_010961010.1 MCA_RS08650 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q93YB2 (503 letters) >NCBI__GCF_000008325.1:WP_010961010.1 Length = 491 Score = 327 bits (838), Expect = 6e-94 Identities = 181/472 (38%), Positives = 266/472 (56%), Gaps = 10/472 (2%) Query: 12 INGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATASG 71 I+G W +K V +PAT + D+PA + A+AAA+ A T W + Sbjct: 19 IDGQWVDADHSKTFSVTDPATGRALADVPAMGAAETMRAIAAAEHAWT-----GWRGKTA 73 Query: 72 AVRARYLRAIAAKVTEKKPELAKLESIDCGKPLDEAAWDIDDVAGCFEYYADLAEKLDAR 131 RA LR + +LA++ + + GKPL EA +I AG E++A+ A + Sbjct: 74 KERAAVLRRWYELILSHTEDLARILTAEQGKPLTEARNEIGYAAGFVEWFAEEAGRAYGE 133 Query: 132 QKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSELAS 191 + P+ + V+R+PIGV ITPWN+P M T K+APALAAGC ++KP+E Sbjct: 134 T---IPSPVPDKRLLVIRQPIGVCAAITPWNFPAAMITRKIAPALAAGCTVVVKPAEQTP 190 Query: 192 LTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTAAA 251 LT L L ++ + G PPGV+N++TG G L ++P + K++FTGS+ G +M A Sbjct: 191 LTALALADLAVQAGFPPGVINVVTGDPEAIGGELTSNPLIRKLSFTGSTEVGRLLMAQCA 250 Query: 252 QLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILHESIATEFL 311 VK +SLELGG +P +VFED DLD A E A+ + GQ C T+R ++ +SI F Sbjct: 251 ATVKKISLELGGNAPFIVFEDADLDAAVEGALLSKYRNTGQTCVCTNRFLIQDSIYDAFA 310 Query: 312 NRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGSRPEHLKK 371 R+ ++ +++ + L+EG GP++ E K+ + +++A GA +L GG R H Sbjct: 311 ERLAAKVRRLEVGNGLDEGVVQGPLIDEQALAKVERHIADALDRGARVLAGGGR--HPLG 368 Query: 372 GFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAAVISNDLE 431 G F +PT++ DVT M REE FGPV + F +EEEA+ +AN T YGL A + DL Sbjct: 369 GRFFQPTVLVDVTPEMLCTREETFGPVAPLLRFGSEEEALAIANATEYGLAAYFYTRDLA 428 Query: 432 RCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVK 483 R RV +A + G+V +N + AP+GGVK+SG GRE G+D YL +K Sbjct: 429 RAFRVGEALEYGMVGINTGMLSYDVAPFGGVKQSGIGREGSHHGMDEYLELK 480 Lambda K H 0.318 0.135 0.416 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: 598 Number of extensions: 27 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: 503 Length of database: 491 Length adjustment: 34 Effective length of query: 469 Effective length of database: 457 Effective search space: 214333 Effective search space used: 214333 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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