Alignments for a candidate for metH in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Desulfotalea psychrophila LSv54

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_011189443.1 DP_RS11245 dihydropteroate synthase

Query= metacyc::G18NG-11090-MONOMER
         (1221 letters)



>NCBI__GCF_000025945.1:WP_011189443.1
          Length = 807

 Score =  565 bits (1456), Expect = e-165
 Identities = 330/871 (37%), Positives = 499/871 (57%), Gaps = 77/871 (8%)

Query: 352  VASLYTSVPLSQETGISMIGERTNSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDL 411
            V+SL+ +V + Q+    ++GER N  GSK FRE +L+ D+E C+ +AK Q   GAH+LD+
Sbjct: 13   VSSLFQAVDIHQQIPPLIVGERANPTGSKKFRELLLAEDFEGCLQVAKDQEELGAHVLDV 72

Query: 412  CVDYVGRDGTADMATLAALLATSSTLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGD 471
            C  + GRD   D+  L    + +   P+MIDST P  I+  LE   GR I+NS+N EDG 
Sbjct: 73   CAAWAGRDEVTDITRLIKDYSGTLKTPLMIDSTNPRAIKAALEVYPGRPIINSINLEDGG 132

Query: 472  GPESRYQRIMKLVKQHGAAVVALTIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIV 531
                    ++ L K++GA V+ALTIDE G A + + K+ IAKR+    T  YGLD  D+ 
Sbjct: 133  ---KTLHEVLTLTKKYGATVIALTIDESGMALSCDEKISIAKRIHHIATTEYGLDSSDLF 189

Query: 532  VDCLTFPISTGQEETRRDGIETIEAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSV 591
             D LTF + +G +  +   ++T++AI+ +K   P  HT LGLSNISFGL PAAR+VLN+V
Sbjct: 190  FDPLTFTVGSGDKTLKDAAVQTMDAIKRIKVELPNCHTILGLSNISFGLPPAARKVLNAV 249

Query: 592  FLNECIEAGLDSAIAHSSKILPMNRIDDRQREVALDMVYDRRTE-DYDPLQEFMQLFEGV 650
            FL+E +  GLD+ I + +  +P++ ID R RE+ALD++Y+R  E + +PL  +++ F   
Sbjct: 250  FLHEAVAIGLDAVIINPTNCIPLDSIDKRARELALDLLYNREVEGESEPLMRYIEYFAEN 309

Query: 651  SAADAKDARAEQLAAMPLFERLAQRIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMK 710
            +A   ++   E+L +    E + + I+ G + GLED ++  + + +P+ IIN+ L+  M+
Sbjct: 310  AAVGDQEGSPEELLSPE--EGIRKAILKGSREGLEDTMQILLDQYTPLDIINQLLVPSMR 367

Query: 711  TVGELFGSGQMQLPFVLQSAETMKTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGD 770
             VGELFG+G+M LPFVL+SAE M+ +V  LEP+ME+ A +  +       KI++ATV+GD
Sbjct: 368  EVGELFGAGEMLLPFVLKSAEIMRASVDILEPYMEKAANSEST-------KILLATVQGD 420

Query: 771  VHDIGKNLVDIILSNNGYDVVNLGIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKEN 830
            VHDIGKNLV+IILSNNGY V+++GIK  + +++EAA+ H+ D+I +SGLLVKS +VM+E+
Sbjct: 421  VHDIGKNLVNIILSNNGYQVIDIGIKASIESIIEAAKRHEVDMICLSGLLVKSAIVMQES 480

Query: 831  LEEMNNAGASNYPVILGGAALTRTYVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRG 890
            +     AG +  P++LGGAALT+ +V       Y   V Y +DAF GL  + +       
Sbjct: 481  MPIYREAGLTQ-PILLGGAALTKKFVAEACAPNYPSPVVYCQDAFSGLAAIQQ------- 532

Query: 891  EGLDPNSPEAIEQAKKKAERKARNERSRKIAAERKANAAPVIVPERSDVSTDTPTAAPPF 950
                 +    +E  K +A      + ++ I           I+P R     D PT  PP 
Sbjct: 533  -----HEAGTLETTKWQARETQEVKEAKTI----------TILPAR-----DIPT--PPL 570

Query: 951  WGTRIVKGLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRL 1010
               R    +  ++FL  +    LF G+WG +  +      Y  L+ TE  P+      R+
Sbjct: 571  --GRAELSVATSDFLDLVKTNTLFRGRWGYRQNK-MSNDEYAQLISTEVMPQFENIRRRI 627

Query: 1011 KSEGILDHVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRP 1070
              E +     + YG+F    +GD + +L+           F  PRQ+ G  LC+AD+ R 
Sbjct: 628  LEEELF-QAKIRYGWFRCYRQGDSLTVLD-----GEREYNFPLPRQKHGPHLCLADYFRD 681

Query: 1071 REQAVKDGQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHS 1130
                 K+G  DV+ F + T+G  +A    +L++   Y +Y  +HG+ V   EALAE+ H 
Sbjct: 682  -----KNGGGDVVGFFVCTIGKKVAQALQQLYSTESYHDYFLLHGLSVNAAEALAEHAHL 736

Query: 1131 RVRSELKLNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRI 1190
             +R ++     GS                + G R+SFGY +CPDL+ +  L ELL+  +I
Sbjct: 737  WMRQQM-----GS---------------QFGGKRYSFGYSACPDLDLQRPLFELLQAEKI 776

Query: 1191 GVELSEELQLHPEQSTDAFVLYHPEAKYFNV 1221
            G+ LSEELQ+ PEQS  A V++H +A YF V
Sbjct: 777  GITLSEELQMVPEQSVSAMVVHHDQASYFVV 807


Lambda     K      H
   0.316    0.135    0.386 

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: 2096
Number of extensions: 100
Number of successful extensions: 11
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: 1221
Length of database: 807
Length adjustment: 44
Effective length of query: 1177
Effective length of database: 763
Effective search space:   898051
Effective search space used:   898051
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 (21.6 bits)
S2: 57 (26.6 bits)

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_011189442.1 DP_RS11240 homocysteine S-methyltransferase family protein

Query= metacyc::G18NG-11090-MONOMER
         (1221 letters)



>NCBI__GCF_000025945.1:WP_011189442.1
          Length = 316

 Score =  229 bits (583), Expect = 3e-64
 Identities = 121/309 (39%), Positives = 185/309 (59%), Gaps = 4/309 (1%)

Query: 26  VLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEAGADLVETNT 85
           +LI DGA GT LQ  ++     + DL GCNE LN + P+ + ++H+ + EAGA +VETNT
Sbjct: 8   LLIFDGACGTTLQSMNI-APSAWGDLAGCNEFLNISAPEYIIELHKKFLEAGAMVVETNT 66

Query: 86  FGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGPGTKLPSLG 145
           FG +   L +Y + ++  E+  +    A++   ++    +   R++ GS+GP TKLPSLG
Sbjct: 67  FGASSIVLTEYGLENKVDEINREAVKNAKKAISQLKD--SSQPRYIAGSIGPTTKLPSLG 124

Query: 146 HAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELDTFLPIICH 205
           H     L    +E  + +++ G DA ++ET QDLLQ+K A+    + +      LP++  
Sbjct: 125 HIETKVLAQSIREQVISLLEAGVDALIVETCQDLLQLKTALISCFEILDVAPKKLPVLAS 184

Query: 206 VTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHADIPVSVMP 265
           VT E  GTML+G++I A    L P  +  +GLNCATGP +M   ++YLS+  D  +S +P
Sbjct: 185 VTFEKQGTMLLGTDIAAVCATLAPFPLFSLGLNCATGPTDMVSQIQYLSQTWDKRISCIP 244

Query: 266 NAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVRDAVVG-VP 324
           N G+P L      YPL  E+ +Q +  FV+EYG+S+VGGCCGT PEHIR +   + G  P
Sbjct: 245 NQGMPELKDGKTHYPLSPEEYSQHMLKFVAEYGVSIVGGCCGTGPEHIRQLATCLRGQKP 304

Query: 325 EQETSTLTK 333
           +++  T T+
Sbjct: 305 QRQLQTNTE 313


Lambda     K      H
   0.316    0.135    0.386 

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: 821
Number of extensions: 36
Number of successful extensions: 3
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: 1221
Length of database: 316
Length adjustment: 37
Effective length of query: 1184
Effective length of database: 279
Effective search space:   330336
Effective search space used:   330336
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 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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