Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 246 bits (628), Expect = 1e-69 Identities = 154/472 (32%), Positives = 249/472 (52%), Gaps = 14/472 (2%) Query: 15 LIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGARM 74 LIDG+WV + + D++NPA ++A V AAE AI AAHRA W R Sbjct: 15 LIDGQWVRGEAS--FDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAARTAKERG 72 Query: 75 RIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFAEN 134 I+ + LI H+ +A ++++EQGK +A+A+G++ G ++ G Sbjct: 73 AILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYGHTIPT 132 Query: 135 VAGGVDTYTLRQPIGVCAGITPFNFP-AMIPLWMFPMAIACGNTFVLKPSEQDPMSTMLL 193 G +++QP+GVCA I P+NFP AMI + P A+A G T V+KP+ + P+S + + Sbjct: 133 PMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGP-ALAAGCTVVVKPAAETPLSALAI 191 Query: 194 VELAIEAGIPPGVLNVV--HGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKR 251 LA EAG+P GVLN+V +V LC ++ +SF GST +G +Y K+ Sbjct: 192 ARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCAGTMKK 251 Query: 252 VQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCM-ATSVVVLVGAAKQWLPDLKA 310 + +G +V DA+ E A++ + + + AGQ C+ A ++V G + L Sbjct: 252 LSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFAARLAE 311 Query: 311 LAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGNF 370 LKV G+ G +GP+I+++A +++ L+ ++ GA++ L G D+ G G+F Sbjct: 312 KVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEV-LTGGDVHGLG---GHF 367 Query: 371 VGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAAR 430 PT+ G TPEM+I+ +EIFGPV +++ +T +A+ L NA PFG +++ Sbjct: 368 YQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGRCW 427 Query: 431 KFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTK 482 + +I+ G VGIN + + F G + S LG G + + Y +TK Sbjct: 428 RVAEQIEAGMVGINEGL-ISTEVAPFGGVKESGLGREG--ASEGLDEYLETK 476 Lambda K H 0.319 0.135 0.397 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: 601 Number of extensions: 32 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: 505 Length of database: 485 Length adjustment: 34 Effective length of query: 471 Effective length of database: 451 Effective search space: 212421 Effective search space used: 212421 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 (21.7 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:
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