Alignments for a candidate for metE in Desulfurobacterium atlanticum DSM 15668

GapMind for Amino acid biosynthesis

Alignments for a candidate for metE in Desulfurobacterium atlanticum DSM 15668

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_089323700.1 CHB58_RS08590 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase

Query= BRENDA::Q9X112
         (734 letters)



>NCBI__GCF_900188395.1:WP_089323700.1
          Length = 720

 Score =  735 bits (1898), Expect = 0.0
 Identities = 394/745 (52%), Positives = 514/745 (68%), Gaps = 41/745 (5%)

Query: 1   MKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNE 60
           +K YA+GFP++G++REFK  +E +W GK+TEE+ +E +  L     + YR  VD  P  E
Sbjct: 2   VKTYAYGFPRLGKQREFKTLIESYWSGKLTEEELKEGIKNLNEKREKTYRSYVDAFPQGE 61

Query: 61  LSYYDFVLDTAVMVGAVPERFGEYRG--LSTYFDMARGGKALEMTKFFNTNYHYLVPEIE 118
           ++ YD + DTA++       FG Y+   L  YF + RG  ALEMTK+FNTNYHYLVP+ E
Sbjct: 62  MTLYDNLFDTALI-------FGIYKADTLDEYFSLCRGKNALEMTKWFNTNYHYLVPDFE 114

Query: 119 --TEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLES 176
              +EF +  NK  E         I+ + ++IGPFT L LSK   E      +   LL+S
Sbjct: 115 GKEKEFSISWNKHEE---------IKESAYLIGPFTLLKLSKNLPE-----GKFAALLKS 160

Query: 177 LVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFP--LTVFTYYD 234
           L   Y E F+    NG K + ++EPAFV +L     + I + Y    +    + VFTYYD
Sbjct: 161 LACKYAEYFKL---NGFKSVHLDEPAFVMELSDKEIEAIKDAYSVFEDIDTKINVFTYYD 217

Query: 235 SVSDYEACVSLPVKRLHFDFVSNE-ENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKV 293
           SV + +    LPV  +  D V +  ENL  L+    P+ K L AGVI+GR  W+ DL + 
Sbjct: 218 SVDNLQFVFDLPVAGVGIDLVHDRGENLSQLDSVD-PKGKTLFAGVIDGRNVWRADLFEK 276

Query: 294 ASLVEKLGAS---AISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLE 350
           A +V+KL       ++N+ PLFHLPV L+    LP  L  K+AFA+EKL+ELK++ D LE
Sbjct: 277 AEIVKKLSEKFEVVVTNAAPLFHLPVNLK-GATLPEELVAKVAFAEEKLKELKLISDVLE 335

Query: 351 G---KTFDLPNVSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTT 407
           G   K  +      + F V     ERVRNL ++ F +   Y ER ++Q+E L LPLFPTT
Sbjct: 336 GDDAKAKEWVEGISKAFGVRENVRERVRNLTDEDFNKAVPYAERIKLQQEILKLPLFPTT 395

Query: 408 TIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTD 467
           TIGSFPQT EVR++R   RKG+++ E+Y+ FIK +I KAI++QEE+G+DV VHGEFER+D
Sbjct: 396 TIGSFPQTQEVRRVRLLNRKGQLADEDYKTFIKGEIAKAIKIQEELGVDVFVHGEFERSD 455

Query: 468 MVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVK 527
           MVEFFAEKL GIATT NGWV+SYG+R YRPPII+G V R EPMT++EI +AQSLT+KPVK
Sbjct: 456 MVEFFAEKLEGIATTGNGWVISYGTRSYRPPIIFGDVERIEPMTVEEIAFAQSLTDKPVK 515

Query: 528 GMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPI 587
           GMLTGPVTI++WSY REDIP  E+AYQI LA+ +E+ D E+AGIKIVQIDE AFREKAPI
Sbjct: 516 GMLTGPVTIIAWSYCREDIPVSEVAYQIGLALRDEIADYEKAGIKIVQIDEAAFREKAPI 575

Query: 588 KKSKWPEYFEWAINAFNLA-ANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRS 646
           KK  W EYF+WA+ +F +  A ++PETQIH+HMCYS+F EIIEYI  ++FDVISIEASRS
Sbjct: 576 KKRNWDEYFDWAVKSFRVCHAKSKPETQIHSHMCYSEFGEIIEYILAMDFDVISIEASRS 635

Query: 647 KGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGL 706
           KG+II AFE    + +QIG+GVWDIHSP VPS++EM+EIVER L+V+PKE  W+NPDCGL
Sbjct: 636 KGDIIEAFEKV-NFDRQIGLGVWDIHSPYVPSVDEMKEIVERALKVIPKENFWVNPDCGL 694

Query: 707 KTRNWDEVIPSLRNMVALAKEMREK 731
           KTR W+E IP++RN+V LA  +RE+
Sbjct: 695 KTRRWEECIPAIRNIVKLANTLREE 719


Lambda     K      H
   0.318    0.137    0.405 

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: 1557
Number of extensions: 74
Number of successful extensions: 13
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: 734
Length of database: 720
Length adjustment: 40
Effective length of query: 694
Effective length of database: 680
Effective search space:   471920
Effective search space used:   471920
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: 55 (25.8 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis