Align serine hydroxymethyltransferase subunit (EC 2.1.2.1) (characterized)
to candidate AZOBR_RS10015 AZOBR_RS10015 serine hydroxymethyltransferase
Query= metacyc::MONOMER-4244 (434 letters) >FitnessBrowser__azobra:AZOBR_RS10015 Length = 425 Score = 621 bits (1601), Expect = 0.0 Identities = 299/420 (71%), Positives = 353/420 (84%) Query: 14 RFFKSHVSETDPDIFSAIQKEFGRQQHEIELIASENIVSQAVLDAAGSVLTNKYAEGYPG 73 RFF + ++ETDP++ A++ E RQQ +IELIASENIVSQAVL+A GSV+TNKYAEGYPG Sbjct: 3 RFFAASLAETDPELARAVRDELVRQQEQIELIASENIVSQAVLEAQGSVMTNKYAEGYPG 62 Query: 74 KRYYGGCQYVDIVEDIAIDRAKKLFNCEFANVQPNSGSQANQGVFNALAQPGDTILGLSL 133 +RYYGGC+YVD+ E +AI+RA KLF C FANVQPNSGSQANQ V AL QPGDTILG+SL Sbjct: 63 RRYYGGCEYVDVAETLAIERACKLFGCGFANVQPNSGSQANQAVNLALLQPGDTILGMSL 122 Query: 134 AAGGHLTHGAPVNQSGKWFKAVHYMVKPDSHLIDMDEVRKLAQEHKPRIIIAGGSAYPRK 193 AAGGHLTHGA N SGKWFKAV Y V+ D HLID DEV +LA+EHKP++IIAGGSAYPR Sbjct: 123 AAGGHLTHGAAPNLSGKWFKAVQYGVRRDDHLIDFDEVERLAREHKPKLIIAGGSAYPRV 182 Query: 194 IDFAAFRAIADEVGAIFLVDMAHFAGLVAAGLIPSPFPHAHVVTTTTHKTLRGPRGGMIL 253 +D+ FRAIADEVGA F+VD+AH+AGL+A G+ P+PFP+A VVTTTTHKTLRGPRGGM+L Sbjct: 183 LDYQRFRAIADEVGAYFMVDIAHYAGLIAGGVYPNPFPYADVVTTTTHKTLRGPRGGMVL 242 Query: 254 TNDADIAKKINSAIFPGIQGGPLMHVIAGKAVAFGEALRPDFKVYIKQVMDNARALGEVL 313 TN +IAKKINSA+FPG+QGGPLMHVIA KAVAF EALRP+FK Y K V+DNARAL +VL Sbjct: 243 TNSEEIAKKINSAVFPGLQGGPLMHVIAAKAVAFAEALRPEFKTYAKSVLDNARALSKVL 302 Query: 314 VQNGFALVSGGTDTHLVLVDLRPKKLTGTKAEKALGRANITCNKNGIPFDPEKPMVTSGI 373 ++ G +VSGGTD+H+VLVDLRPK LTG AE +L A +TCNKNG+PFDP+KPMVTSG+ Sbjct: 303 IEGGLDIVSGGTDSHIVLVDLRPKNLTGKAAEASLEHAGMTCNKNGVPFDPQKPMVTSGV 362 Query: 374 RLGSPAGTTRGFGVAEFQEIGRLISEVLDGVAKNGEDGNGAVEAAVKAKAIALCDRFPIY 433 RLGSPA TTRGFGVAEF+++GRLI E LDG+A + N AVEA V+ + LC RFPIY Sbjct: 363 RLGSPAATTRGFGVAEFEQVGRLIVETLDGLAASNSGDNAAVEAKVREEVRELCRRFPIY 422 Lambda K H 0.319 0.136 0.396 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: 616 Number of extensions: 22 Number of successful extensions: 1 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: 434 Length of database: 425 Length adjustment: 32 Effective length of query: 402 Effective length of database: 393 Effective search space: 157986 Effective search space used: 157986 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: 51 (24.3 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