Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_5146 (508 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Length = 512 Score = 253 bits (645), Expect = 1e-71 Identities = 172/493 (34%), Positives = 244/493 (49%), Gaps = 25/493 (5%) Query: 7 PNDTTVQKVKLLIDGQWVESKTTEWHDIINPA-TQQVLAKVPFATAEEVDAAISAAHRAF 65 P TT LI G W + T + NP+ T+ V+ A+ E+ A++AAH AF Sbjct: 27 PPHTTTAMHANLIGGAWTDGVRT--YQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAF 84 Query: 66 QTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHACS 125 W L+ R I+ + I + +L+ E+GKT+ +A G++ R + + Sbjct: 85 PAWSLSTPQQRFDILDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAG 144 Query: 126 IGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKP 185 GE +V GV R+P+G ITP+NFP IP W A+A GN V KP Sbjct: 145 EALRPGGEVMPSVRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKP 204 Query: 186 SEQDPMSTMLLVELAIEAGIPAGVLNVVHG-GKDVVDGLCTHKDIKAVSFVGSTAVGTHV 244 +E P S L ++ AG+PAGV N+V G G DV L + I VSF GS G V Sbjct: 205 AEVVPGSAWALADILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRV 264 Query: 245 YDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATS-VVVLVGA 303 G +VQ MG KN VVL DA+ A+ A + +GF + GQRC A+S V+V G Sbjct: 265 AAACVPRGAKVQLEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGI 324 Query: 304 AKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDGREI 363 +++ + + LKV+ + GTD+GPV+ + A+ L+ I G +EGAKL G + Sbjct: 325 HDRFVAAMVEKMKTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEAL 384 Query: 364 -----SVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPF 418 PG+ ++ P LF+ T M+I +EIFGPV+ VL +EA+AL N PF Sbjct: 385 EKNADGAPGF----YLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPF 440 Query: 419 GNGTGLFTQSGAAARKFQNEIDVGQVGINIP---IPVPVPFFSFTGSRGSKLGDLGP--Y 473 G +G+ T S A F+ G V +N+P + VPF G K GP Sbjct: 441 GLASGIATTSLKHATHFKRHAQAGMVMVNLPTAGVDYHVPF------GGRKSSSYGPREQ 494 Query: 474 GKQVVQFYTQTKT 486 G+ +FYT KT Sbjct: 495 GRYAAEFYTTVKT 507 Lambda K H 0.318 0.135 0.395 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: 669 Number of extensions: 38 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: 508 Length of database: 512 Length adjustment: 34 Effective length of query: 474 Effective length of database: 478 Effective search space: 226572 Effective search space used: 226572 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 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