Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate WP_022949137.1 H035_RS19450 cytochrome c biogenesis protein CcmH
Query= BRENDA::Q9L072 (480 letters) >NCBI__GCF_000421465.1:WP_022949137.1 Length = 538 Score = 514 bits (1324), Expect = e-150 Identities = 269/483 (55%), Positives = 332/483 (68%), Gaps = 12/483 (2%) Query: 2 RSHLLNDTTAEQYRRSVTEGVERVAAKLATTDRPFTGVTVDALSPRIDAIDLDEPLHDTA 61 R L N ++Y+ ++ +G+E V +A + +PFTG L+ R IDLD+ + Sbjct: 25 RDFLFNAQNLKRYKEAILQGLELVHRNIANSRKPFTGTHPHELAERFRDIDLDQSFSRDS 84 Query: 62 AVLDELEDVYLRDAVYFHHPRYLAHLNCPVVIPALLGEAVLSAVNSSLDTWDQSAGGTLI 121 VL E++ +YL DAVYFHHP Y AHLNCPVV+PALLGE + S++N++++TWDQSAG T I Sbjct: 85 EVLAEVQALYLDDAVYFHHPSYAAHLNCPVVVPALLGELIASSINTAVETWDQSAGATFI 144 Query: 122 ERKLIDWTCARIGLGPAADGVFTSGGTQSNLQALLLAREEAKAE------------DFAD 169 E+KLIDWT +IGL ADGVFTSGGTQSNL ALLLAR+ A+ DFA Sbjct: 145 EQKLIDWTAGKIGLQKQADGVFTSGGTQSNLMALLLARDWFCAKRGHDIKTRGLPADFAK 204 Query: 170 LRIFASEASHFSVRKSAKLLGLGPDAVVSIPVDRDKRMQTVALARELERCARDGLVPMAV 229 LRIFASE HFS++K+A LGLG +AV+ +P DR RM AL RE++RC GL+PMAV Sbjct: 205 LRIFASEIGHFSLKKAAATLGLGYEAVIPVPCDRYFRMDPHALRREIKRCQDRGLLPMAV 264 Query: 230 VATGGTTDFGSIDPLPEIAGLCEQYGVWMHVDAAYGCGLLASLKYRDRITGIERADSVTV 289 V+T GTTDFGSIDPLPEIA L G+W+H DAAYGCGLL S K+R + GIE +DSVTV Sbjct: 265 VSTAGTTDFGSIDPLPEIATLGHARGMWVHTDAAYGCGLLVSPKHRHLLRGIELSDSVTV 324 Query: 290 DYHKSFFQPVSSSAVLVRDAATLRHATYHAEYLNPRRMVQERIPNQVDKSLQTTRRFDAL 349 DYHKSFFQPVS SA+LV D L TYHA+YLNPR + E P+ V+KS+QTTRRFDAL Sbjct: 325 DYHKSFFQPVSCSALLVSDKRHLSAVTYHADYLNPRNQLPEGTPDLVNKSMQTTRRFDAL 384 Query: 350 KLWMTLRVMGADGIGVLFDEVCDLAAEGWKLLAADPRFDVVVQPSLSTLVFRHIPADVTD 409 KLW+TLR +GA IG FD V L + + L +DP +V+ QP LSTLVFR P+ Sbjct: 385 KLWLTLRTVGARNIGEAFDRVMHLTRQTYLLFLSDPSIEVIHQPQLSTLVFRFHPSRQHS 444 Query: 410 PAEIDRANLYARKALFASGDAVVAGTKVAGRHYLKFTLLNPETTPADIAAVLDLIAGHAE 469 A +D N RKAL+ SG+A+VAGTKV G HYLK TLLNP T DI VL I H + Sbjct: 445 EAVLDEVNASIRKALYRSGEALVAGTKVRGHHYLKCTLLNPAATIQDIQGVLKRIKQHGQ 504 Query: 470 QYL 472 + L Sbjct: 505 EAL 507 Lambda K H 0.320 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: 659 Number of extensions: 18 Number of successful extensions: 2 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: 480 Length of database: 538 Length adjustment: 34 Effective length of query: 446 Effective length of database: 504 Effective search space: 224784 Effective search space used: 224784 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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