Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_012282525.1 HM1_RS06550 carbamoyl phosphate synthase small subunit
Query= curated2:B2URJ0 (372 letters) >NCBI__GCF_000019165.1:WP_012282525.1 Length = 439 Score = 330 bits (845), Expect = 6e-95 Identities = 180/418 (43%), Positives = 242/418 (57%), Gaps = 61/418 (14%) Query: 3 AILALEDGSVFIGSHFGATGTEVGEACFNTSMTGYQEVLTDPSYSGQIVTMTYPLIGNYG 62 A L LEDG++F G FG G+ GE FNT MTGYQEVLTDPSY+GQIVTMTYPLIGNYG Sbjct: 9 AYLLLEDGTLFKGIPFGYRGSSTGEVVFNTGMTGYQEVLTDPSYAGQIVTMTYPLIGNYG 68 Query: 63 VNPEDGESGKAQVSGFVVAELAKVHSNWRATESLGPWLEKQGVIGIEGVDTRKIAKHLRS 122 +N D ES K QV G++V E SN+R+ ++L +L + + G+ G+DTR + + +R Sbjct: 69 INAGDAESAKPQVRGYIVREACARPSNYRSEKTLDHYLAQHRIPGLAGIDTRSLTRRIRE 128 Query: 123 AGAMRACL---TTELTPEEAVEAARNAPSMEGCNIV-DKIG--SHPMTPEEVDALVTGKT 176 G +R + L+ +A+ + S++G N D+ G S P E +AL +T Sbjct: 129 HGTLRGAIINGANSLSNGQALNGTNGSASVKGFNSANDRYGMSSADAAPWEGEALANLRT 188 Query: 177 -------------------------------------------------LPPAEYDIVAF 187 +P + + Sbjct: 189 GARTSLEAIFAQMDEASYTCWIEYLTAVRNLPVAGPHLVSSVTTPQAYVIPGDGFRVAVL 248 Query: 188 DFGIKYNILRQLRENGFRVTVVPAHTTAEEVLAMNPDGVFLSNGPGDPATLTDIHREVAA 247 DFGIK NILR L+ + V PAH AEE+ A NPDG+FLSNGPGDP + ++ Sbjct: 249 DFGIKENILRMLKALDCHLMVFPAHAPAEEIGAANPDGLFLSNGPGDPKDVAPAIETISH 308 Query: 248 LIGK------VPMFGICLGHQIISHALGAKTFKLKFGHRGANHPVKDLKTGKISITSQNH 301 + +P+FGICLGHQ++ A GA T+KLKFGHRGANHPVKDL+TG++ ITSQNH Sbjct: 309 FLRPGTTARPLPIFGICLGHQLLGLAAGADTYKLKFGHRGANHPVKDLRTGRVFITSQNH 368 Query: 302 GFAVDPDTVPDDVEITLINLNDNTVEGIAHRTLPVFSVQYHPEAAPGPRDPQYLFRDF 359 G+A+D +T+P ++ N ND+TVEG+ H+ LP++SVQYHPEAAPGP D +LF +F Sbjct: 369 GYAIDENTLPKGFTVSHRNGNDDTVEGLRHQHLPLYSVQYHPEAAPGPHDSAFLFDEF 426 Lambda K H 0.317 0.135 0.401 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: 542 Number of extensions: 27 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 372 Length of database: 439 Length adjustment: 31 Effective length of query: 341 Effective length of database: 408 Effective search space: 139128 Effective search space used: 139128 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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