Align Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= curated2:A8GHZ8 (474 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 296 bits (758), Expect = 1e-84 Identities = 177/475 (37%), Positives = 267/475 (56%), Gaps = 7/475 (1%) Query: 1 MQSQLLINGQLVTGQGALLPVYNPATGEVVVQVAEASAEQVDQAVLAADAAFEHWGQTTP 60 +++ LI+GQ V G+ A V NPA G ++ VA+ A + A+ AA A W T Sbjct: 10 VETAALIDGQWVRGE-ASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAARTA 68 Query: 61 KERAEHLLKLADLIDSHAETFARLESINCGKPYHCVLNDELPGVADVFRFFAGASRCLSG 120 KER L + +DLI +HA+ ARL + GKP + + G A +FA ++ G Sbjct: 69 KERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYG-ASFIDWFAEEAKRAYG 127 Query: 121 LAAGEYLAGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEQTPLT 180 + G + P+GV A+IAPWN+P+ M K+ PALAAG VV+KP+ +TPL+ Sbjct: 128 HTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLS 187 Query: 181 TFKLAELA--AGLFPPGVLNVLFG-RGASVGDRLTGHNKVRMVSLTGSIATGEHIIGHTA 237 +A LA AG+ P GVLN++ R + VG L ++VR +S TGS G+ + A Sbjct: 188 ALAIARLATEAGV-PAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCA 246 Query: 238 SGIKRTHMELGGKAPVLVFDDADLQQVVEGIRSFGFYNAGQDCTAACRIYAQKGIYPQLV 297 +K+ +ELGG AP +VFDDADL+ V+G + + NAGQ C A R+ Q GI+ Sbjct: 247 GTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFA 306 Query: 298 KALGEAIGSLKIGPPIDASSELGPLITAQHLERVVGFVERAKALPHVQVVTGGERVNGPG 357 L E + +LK+GP ++GPLI + L +VVG V A +V+TGG+ G Sbjct: 307 ARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGA-VQAGAEVLTGGDVHGLGG 365 Query: 358 YYFQPTLLAGARQEDEIVQREVFGPVVTVTPFDDEAQVLAWANESDYGLASSLWTRDVGR 417 +++QPT+L GA E I Q E+FGPV + F+ EA+ + AN + +GLA+ ++RDVGR Sbjct: 366 HFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGR 425 Query: 418 AHRLSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTAIRHVMF 472 R++ +++ G +N + P GG K SG G++ + GL++Y +++ F Sbjct: 426 CWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLCF 480 Lambda K H 0.320 0.136 0.410 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: 517 Number of extensions: 25 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: 474 Length of database: 485 Length adjustment: 34 Effective length of query: 440 Effective length of database: 451 Effective search space: 198440 Effective search space used: 198440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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