Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate 6938573 Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >FitnessBrowser__SB2B:6938573 Length = 1058 Score = 172 bits (437), Expect = 4e-47 Identities = 155/487 (31%), Positives = 237/487 (48%), Gaps = 25/487 (5%) Query: 15 LIDGEWVESQTTEWHDIVNPA-TQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGAR 73 L++GE + + D+V+P T + +V FA A ++ AI+ A +AF +W TP+ R Sbjct: 568 LVNGETLSGEV---RDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETR 624 Query: 74 MRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMG--EF 131 + KL L+ E+ + + + + E GK+I D ++ ++ + M E Sbjct: 625 ANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPEL 684 Query: 132 AENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTM 191 G ++ L Q GV I+P+NFP I L A+A GNT + KP+EQ + Sbjct: 685 LPGPTGELNELFL-QGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGF 743 Query: 192 LLVELAIEAGIPPGVLNVVHGGKDVVDA-LCTHKDIKAVSFVGSTAVGTHV-YDLAGKHG 249 V+LA EAGIP VL + G VV A L + + I V F GST + LAG+ G Sbjct: 744 RAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDG 803 Query: 250 KRVQ--SMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL-VGAAKQWLP 306 + + G +N VV + EQ +N +V + F +AGQRC A V+ L A++ L Sbjct: 804 AIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLD 863 Query: 307 DLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVP-GY 365 LK +L + TDVGPVI AKA + I+ IK+ +L +S+P G Sbjct: 864 VLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDH-IKQVGRLI---HQLSLPEGT 919 Query: 366 EKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDT--LDQAIALVNANPFGNGTGLFT 423 E G+FV PT +++ T+E FGP+L V+ L + I +N+ FG G+ + Sbjct: 920 ENGHFVAPTAVE--IDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHS 977 Query: 424 QSGAAARKFQTEIDVGQVGIN---IPIPVPVPFFSFTGSRGSKLGDLGP-YGKQVVQFYT 479 ++ A + +++VG V IN I V V F G G+ GP Y + V T Sbjct: 978 RNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKT 1037 Query: 480 QTKTVTA 486 +T +TA Sbjct: 1038 RTNNITA 1044 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: 1049 Number of extensions: 50 Number of successful extensions: 5 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: 1058 Length adjustment: 40 Effective length of query: 465 Effective length of database: 1018 Effective search space: 473370 Effective search space used: 473370 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: 55 (25.8 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