Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate WP_014449805.1 LFE_RS08455 homocysteine S-methyltransferase family protein
Query= reanno::DvH:207036 (804 letters) >NCBI__GCF_000284315.1:WP_014449805.1 Length = 828 Score = 561 bits (1446), Expect = e-164 Identities = 321/796 (40%), Positives = 482/796 (60%), Gaps = 12/796 (1%) Query: 14 LLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTTNTFGGSRFKL 73 LL DG +G +LQ+RGLPAG +P+ + +++P ++ +H +YV AG+DI+ TNTFG SR +L Sbjct: 13 LLLDGSMGALLQSRGLPAGYAPDLWNIEKPQEIQAVHTEYVNAGSDIILTNTFGASRLRL 72 Query: 74 GDGFDVVDFNRRMAAIAREAADASGR-QAFVAGSIGPTGHFVKPLGEVEPAALVAAFREQ 132 + ++ D R + A + A + R +A+VAG IGP+G + P G++ +A F EQ Sbjct: 73 SE-YNAQDRIREINFQAVDLAQRASRGKAYVAGDIGPSGTTIAPFGDLPFDDAIAIFYEQ 131 Query: 133 VRGLVAGGADLLMIETQFDLAEARAAVVAARAECS--LPIAVSMTFE-NGVSLTGSTPEV 189 + L+ GADL+ IET FD+ E RAA++ R + +P+ MTF +G++ +GS PE Sbjct: 132 AKLLLEAGADLIAIETMFDIQEMRAALIGVREATNGRIPLMALMTFNMDGITDSGSDPET 191 Query: 190 FVATMLNLGVDLLGTNCSAGPDQMHDVVASLLASASVPVLVEPNAGLPELIDGKTVFRLP 249 + + GVD++G NCS GP+ M VV+ L + + VEPNAGLP +G+T++ Sbjct: 192 AASVLEGFGVDIMGLNCSVGPEAMVPVVSRLGQTTDTFIAVEPNAGLPVHRNGETLYLTG 251 Query: 250 PAPFAEKTAAFAAMGARVLGGCCGTTPDHIAALRQAVADI-PATLPVDSGVGIVLTTRSH 308 A+ +F GA ++GGCCGTTP++I L + V P + P S + I ++R+ Sbjct: 252 AEEVAKFAPSFVEAGANIIGGCCGTTPEYIRILAKTVKGASPISRPTPSLLKI--SSRTS 309 Query: 309 LVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEAGAPILDVNVGAPM 368 + +G P I+GE+INPTGKK + G L + + ++ EAGA LDVNVG P+ Sbjct: 310 MTLIGDGVPFLIVGEKINPTGKKIFSEAIANGQVDLIVAEARKEAEAGAGALDVNVGVPL 369 Query: 369 VDEEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYCPGSTLVNSISGEPGRMERLGP 428 V+E ++ + + +PL IDSS A+A+E L PG LVNS++ E R+E + P Sbjct: 370 VNEAEMMAKAITAIQNVVSLPLVIDSSYASALESGLKLYPGRALVNSVNAEDERLEEVLP 429 Query: 429 LCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEGLGIPRRLVMVDVLALAVSSKA 488 L R +GA I L + G +P A ER+ E++L +AE LG+ R ++ D LAL VS+ Sbjct: 430 LIRKYGAAVIAL-VSGDNIPETAAERMKNAEKILRRAEELGLKPRDLIFDTLALTVSAVQ 488 Query: 489 EAARQCLETIRWCTAN-GFATTIGLSNISFGLPARELLNGTFLAMAAGAGLSSCIAHPGN 547 EAA+Q L+TI T +GLSN+SFGLPAR++++ FL+MA GAGL + I P + Sbjct: 489 EAAKQTLDTITLIKKELRLPTILGLSNVSFGLPARKIVHNNFLSMAIGAGLDAAICDPYD 548 Query: 548 GRIRETVACADVLLARDANAERFIDAYAAWTPATQGGPVASGPGLASQPPATTLEEAVVK 607 + +T+A + + RD + +++ AAWTPA QG AS A + + + +A+++ Sbjct: 549 QVLHQTIAASSLFARRDPDCRIYLNKAAAWTPA-QGNHPASKEA-APKTTSEAIRQAILE 606 Query: 608 GDRDGVTAIVESELAAGADPFDLVQTKLIPAINEVGVKYERREYFLPQLIRSAETMQTAF 667 G+RDG+ A+ + L G F + + PAI +G + +R F+P LI A+ M+ Sbjct: 607 GERDGIAALCQKGLDEGLSAFTIFLDIMTPAIRHLGDLFGQRVKFIPHLIAGADAMKKGV 666 Query: 668 RRLQPLLEEMRGAEVRPVIIMATVEGDIHDIGKNIVSLMLGNHGFEVVDLGKDVKAETIV 727 LQP LE E + ++ ATV+GDIHDIGKNI LML N GF V+DLG++V + I+ Sbjct: 667 EVLQPHLEADGPVEPKGCVVFATVKGDIHDIGKNICILMLRNFGFSVIDLGRNVPLDDIL 726 Query: 728 DAAETHGARIIGLSALMTTTMVRMEDTVKLVRARGLDVKVIVGGAVVTKAFADAIGADGY 787 AAE H A+II LSALMTTTM++M+ ++ +R + L KV+VGGAVVT F+ I ADGY Sbjct: 727 AAAEKHQAQIIALSALMTTTMMQMKTAIETIREKNLPYKVMVGGAVVTPKFSTEIKADGY 786 Query: 788 SADAVEAVRLAKSLLA 803 D + V LA+ L++ Sbjct: 787 GKDVGDVVPLAEKLIS 802 Lambda K H 0.320 0.137 0.392 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: 1579 Number of extensions: 82 Number of successful extensions: 9 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: 804 Length of database: 828 Length adjustment: 41 Effective length of query: 763 Effective length of database: 787 Effective search space: 600481 Effective search space used: 600481 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: 56 (26.2 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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