Alignments for a candidate for serA in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Sedimenticola selenatireducens DSM 17993

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_029134612.1 A3GO_RS0118160 FAD-linked oxidase

Query= reanno::HerbieS:HSERO_RS19500
         (1333 letters)



>NCBI__GCF_000428045.1:WP_029134612.1
          Length = 1287

 Score = 1476 bits (3820), Expect = 0.0
 Identities = 750/1319 (56%), Positives = 949/1319 (71%), Gaps = 44/1319 (3%)

Query: 20   PPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRR 79
            P R+REIPYNYTSFSDREIVIR LGEE W +++ LRG R+TGRSARMLYEVLGD+WVV R
Sbjct: 8    PQRIREIPYNYTSFSDREIVIRFLGEEMWQVIETLRGSRRTGRSARMLYEVLGDMWVVVR 67

Query: 80   NPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAA 139
            NPYLQDDLL +  RR ALI+AL HRL + + R         G+ +A R       LL AA
Sbjct: 68   NPYLQDDLLMDTVRRGALIDALKHRLDQFEART-------NGNEDAIR-------LLAAA 113

Query: 140  KKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVL 199
            + A+  F+  F++  DLR++ ++ L + T +DNI F GL+RVSH TDATDWRVE PFVV+
Sbjct: 114  RVAVEKFSACFQRNQDLRRQVSRALSKITRRDNIDFGGLARVSHATDATDWRVEVPFVVI 173

Query: 200  TPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEI 259
             PD E+E+A +V+ACIE GLTIIPRGGGTGYTG A+PL P  AVINTEKLE+LG VE   
Sbjct: 174  CPDREEEVAPIVRACIESGLTIIPRGGGTGYTGSAVPLDPYCAVINTEKLERLGEVEYRE 233

Query: 260  LPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVL 319
            LPG++    T+ +GAGVVTKRVSD A + G  FAVDPTS  AS IGGN+AMNAGGKKAVL
Sbjct: 234  LPGVEGQVPTVETGAGVVTKRVSDLASEHGLAFAVDPTSQNASTIGGNIAMNAGGKKAVL 293

Query: 320  WGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKT 379
            WGT LDNLASWRMV P   WLEV RL+HNLGKIH+ E   F++      +   KT V + 
Sbjct: 294  WGTTLDNLASWRMVMPDSHWLEVERLNHNLGKIHEQERVSFRIT---RYQADGKTRVGEP 350

Query: 380  EILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEF 439
            E+LE+ G  FRK GLGKDVTDKFLSGLPGVQKEGCDGLITSAR+ILH+MP   RTVC+EF
Sbjct: 351  ELLEMPGASFRKAGLGKDVTDKFLSGLPGVQKEGCDGLITSARFILHRMPDHVRTVCMEF 410

Query: 440  FG-QARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVL 498
            FG     A+P+I+EI+D + A     G  + GLEHLDERY++AV Y+TK+ R   PKMVL
Sbjct: 411  FGSDLSRAVPAIIEIRDTIGA---TDGVEMVGLEHLDERYIKAVKYSTKAPRRERPKMVL 467

Query: 499  IGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFK 558
            I D+V DDE+AVA AASEV+R+ N R GEGF+AVSPEAR++FWLDRSRTAAI+ HTNAFK
Sbjct: 468  ITDLVSDDEDAVAKAASEVVRLVNAREGEGFIAVSPEARRRFWLDRSRTAAISAHTNAFK 527

Query: 559  INEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAEGDDI 618
            +NEDVVIPL R+ EY+ GIE+INIE SI NKLQ++  + + ++ G +P  +  +   +  
Sbjct: 528  VNEDVVIPLERLAEYSRGIEQINIEQSISNKLQIMRAVLN-YLGGPMPELRLPEEYEESE 586

Query: 619  PAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVD 678
             +  +L  +   A  ++     RW  +LANL+ P  +    L    L K           
Sbjct: 587  ESRAILRAKRDAACEVVATAEQRWQQILANLESPAEDFTALLREKELAKR---------- 636

Query: 679  QPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALH 738
            Q   ++  ++  R +  ++++EV A+L +IF G     + E   +IH  +   R+FVALH
Sbjct: 637  QAGDSLLDMMLRRDLVHNYRKEVAARLNEIFDGQDMLAVQERLNSIHGEIRDARLFVALH 696

Query: 739  MHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTED 798
            MHAGDGNVHTNIPV+S +YEML ++   V RIM LA+SL+GVISGEHGIG+TK++F+  D
Sbjct: 697  MHAGDGNVHTNIPVHSHNYEMLHESERMVERIMALAKSLDGVISGEHGIGLTKIQFMEAD 756

Query: 799  EIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIA 858
            ++ +F  YK+RVDPE  FN+GKL  +PG  + L  AYTPS  L+  E++I++ S++G + 
Sbjct: 757  KLRDFVAYKERVDPERHFNRGKL--MPG--SSLDGAYTPSLRLVQQEAIILEASELGELN 812

Query: 859  SSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEE 918
              +K CLRCGKCKPVC THVPRANLLYSPRNKIL T L++EAFLYEEQTRRG+S++H+EE
Sbjct: 813  DDIKHCLRCGKCKPVCMTHVPRANLLYSPRNKILGTGLIIEAFLYEEQTRRGISLRHFEE 872

Query: 919  FEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPA 978
              DVADHCT+CHKC+ PCPVDIDFGDV++ MR +L + GKK  N GT AAM FLN TDP 
Sbjct: 873  MNDVADHCTICHKCLNPCPVDIDFGDVTVRMRKILTEQGKKRRNIGTWAAMSFLNTTDPR 932

Query: 979  TINATRKVMTQWGFKAQRLGNDLMKK--FAKKQTQKPPATVGKPPVKEQVIHFINKKMPG 1036
            TI + RK M +WGFK   LG+ L ++     +  Q P AT G+P  K  V+  + + +  
Sbjct: 933  TIRSLRKGMLEWGFKGLALGHALFRRAGMLGRGKQIPHATTGRPEPKALVVELVRRPIRV 992

Query: 1037 NLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWN 1096
             LPKKT RALL IED  ++PI R+P     +++A+FYFPGCGSERLFS VGLAT AML+ 
Sbjct: 993  ELPKKTTRALLGIEDSDMIPIFRDPAKVNDESDAIFYFPGCGSERLFSDVGLATIAMLYE 1052

Query: 1097 VGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTC 1156
            +G + VLPPGYLCCGYPQ   G   KG +I T NRVLFHR+ANTLNY+DIKTVVVSCGTC
Sbjct: 1053 LGNEVVLPPGYLCCGYPQTAAGQHAKGLEITTGNRVLFHRVANTLNYMDIKTVVVSCGTC 1112

Query: 1157 YDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVN 1216
             DQL  YEF+KIFPGCR++DIHEYL+EKGV LE  +GT Y+YHDPCHSPMKQ +P +  +
Sbjct: 1113 IDQLMKYEFDKIFPGCRLLDIHEYLMEKGVVLEHASGTEYLYHDPCHSPMKQYNPTEVAS 1172

Query: 1217 SLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRAD--GFTGD 1274
             L+     +K+  +DRCCGE+GT G +RPD+++Q+R+RK EE+ +G   +  +     G+
Sbjct: 1173 RLMD----KKVLLSDRCCGEAGTLGTARPDIASQLRYRKVEELEQGIKALSGNERAVNGN 1228

Query: 1275 VKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333
            VK+LTSCP+C QGL+RY ++ G    YIV E+ R  LGENW   +VER   GGIER+L+
Sbjct: 1229 VKMLTSCPACTQGLNRYKDETGLEVSYIVEELVRDRLGENWQQGFVERVMKGGIERVLL 1287


Lambda     K      H
   0.319    0.136    0.402 

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: 3982
Number of extensions: 183
Number of successful extensions: 14
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: 1333
Length of database: 1287
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1239
Effective search space:  1592115
Effective search space used:  1592115
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: 59 (27.3 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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