Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate RR42_RS21375 RR42_RS21375 succinate-semialdehyde dehydrogenase
Query= reanno::MR1:199807 (487 letters) >FitnessBrowser__Cup4G11:RR42_RS21375 Length = 488 Score = 203 bits (517), Expect = 9e-57 Identities = 160/472 (33%), Positives = 230/472 (48%), Gaps = 27/472 (5%) Query: 4 FIKGQWHTG-KGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDARL 62 FI GQW + G +NPA+G +I A + A++AAR AQ W R Sbjct: 14 FIGGQWQSADSGATFPVTNPADGSLIGTVPLMGAAETTRAIEAARVAQAAWRRKTARERA 73 Query: 63 KIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTETND 122 +++ A+ + AN +LA + E GKP E E + A KR + Sbjct: 74 QVLRAWYDLMLANADDLAVLMTTEQGKPLAEARGEAVYAASFLEWFAEQA-KRVHGDVLA 132 Query: 123 TPAG--RAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180 TPA R ++ +P GV A P+NFP + PAL AG ++V KP+E TP A + Sbjct: 133 TPASDKRLLVVKEPVGVCAAITPWNFPLAMITRKAGPALAAGCAMVLKPAEDTPLSALAL 192 Query: 181 VTLWEKSGLPAGVLNLVQGE----VDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHP 236 L E++GLPAG+L++V G+ ++ G L P + L FTGS+ G +L +Q A Sbjct: 193 ALLAERAGLPAGLLSVVTGDAASSIEIGAELTGSPVVRKLSFTGSTEVGRILMRQSAPTI 252 Query: 237 GKILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVA 296 K L+LE+GGN P I+ AD+ AAV + S Y ++GQ C CA RLYV + DA Sbjct: 253 KK-LSLELGGNAPFIVFDDADLDAAVEGAMASKYRNAGQTCVCANRLYVHD-KVYDAFAQ 310 Query: 297 KLVEAVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLV-ELMHLQAGT 355 KLV AVK +KVG +P G +I+E A + A+ L G L H GT Sbjct: 311 KLVAAVKTLKVG-HGLEPGVQQGPLINEDAVAKVEQHIADALGKGARLLTGGKRHDLGGT 369 Query: 356 GLVSPGLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSA-------GIL 408 L +VT + +E FGPL L R++ ++ + +AN T +GL++ G + Sbjct: 370 FFEPTVLANVTPDMVVAKQETFGPLAPLFRFTSDEEVVNMANDTEFGLASYFFSRDIGRI 429 Query: 409 ADSREDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAAD 460 E EY + I G++ ++ APFGGV SG R A Y + Sbjct: 430 WRVAEALEYGMVGINTGLI--------SNEVAPFGGVKQSGLGREGASYGIE 473 Lambda K H 0.316 0.133 0.391 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: 603 Number of extensions: 28 Number of successful extensions: 7 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: 487 Length of database: 488 Length adjustment: 34 Effective length of query: 453 Effective length of database: 454 Effective search space: 205662 Effective search space used: 205662 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 (21.6 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