Alignments for a candidate for serA in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Steroidobacter denitrificans DSM 18526

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_210399057.1 ACG33_RS12360 FAD/FMN-binding oxidoreductase

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



>NCBI__GCF_001579945.1:WP_210399057.1
          Length = 1323

 Score = 1904 bits (4933), Expect = 0.0
 Identities = 933/1314 (71%), Positives = 1088/1314 (82%), Gaps = 14/1314 (1%)

Query: 20   PPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRR 79
            P RLREIPYNYTSFSDREIVIRLLGE +W LL+ELRG+R+TGRSARMLYE LGDIWVV+R
Sbjct: 24   PARLREIPYNYTSFSDREIVIRLLGEPAWDLLNELRGERRTGRSARMLYEALGDIWVVQR 83

Query: 80   NPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAA 139
            NPYLQDDL+D+ KRR  L+EAL HRL EV++RR  TD      AE  R+   V  LL+AA
Sbjct: 84   NPYLQDDLVDSAKRRRQLVEALQHRLNEVERRRDDTD------AERDRK---VGELLRAA 134

Query: 140  KKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVL 199
            ++A+  FA+   Q   LRKRA ++L R T  DNI+ D  +RVSHVTDATDWRVEYPF+VL
Sbjct: 135  REAVESFADGLEQVASLRKRARRLLERHTRADNIRLDAFARVSHVTDATDWRVEYPFLVL 194

Query: 200  TPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEI 259
            +PD EDE+  LV+ CIELGLTIIPRGGGTGYTGGA+PLTP +AVINTEKLE LG VE   
Sbjct: 195  SPDGEDEIPALVRGCIELGLTIIPRGGGTGYTGGAVPLTPRAAVINTEKLEALGKVETRP 254

Query: 260  LPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVL 319
            LPG      +I +GAGVVT+RV++AA++AG VFAVDPTSA+ASCIGGNVAMNAGGKKAVL
Sbjct: 255  LPGTTDDAPSILTGAGVVTRRVAEAADRAGLVFAVDPTSADASCIGGNVAMNAGGKKAVL 314

Query: 320  WGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKT 379
            WGTA+DNL  WRMVDP G+WLEVTRL+H+ GKIH+V+ A+F+L W           V +T
Sbjct: 315  WGTAVDNLLWWRMVDPDGNWLEVTRLEHDRGKIHEVDQAKFELVWKDGRAAPAHARVLRT 374

Query: 380  EILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEF 439
             ++ I G++FRK GLGKDVTDKFL GLPGVQKEGCDG+ITSARW+LH+MP   RTVCLEF
Sbjct: 375  GVVAIEGRRFRKAGLGKDVTDKFLGGLPGVQKEGCDGVITSARWLLHRMPNHVRTVCLEF 434

Query: 440  FGQARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLI 499
            FG AR AIPSIVEIK +LDA+ + GG  LAGLEHLDERYLRAVGY+T+SKRG LPKMVL+
Sbjct: 435  FGHARHAIPSIVEIKSHLDAQARSGGVQLAGLEHLDERYLRAVGYSTRSKRGALPKMVLL 494

Query: 500  GDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKI 559
            GDIVGDDE+AVA A SEV+R+AN+R GEGFVAV+PE+R++FWLDRSRTAAIAKHTNAFKI
Sbjct: 495  GDIVGDDEDAVARATSEVVRIANSRSGEGFVAVNPESRRQFWLDRSRTAAIAKHTNAFKI 554

Query: 560  NEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAEGDDIP 619
            NEDVVIPL+RMG+YTD IERINIELS KNKL+LL EL  +F    L LGK +D + +   
Sbjct: 555  NEDVVIPLDRMGDYTDAIERINIELSFKNKLKLLDELLEYF-STELTLGKIEDPDLEHAS 613

Query: 620  AAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVDQ 679
              E L +R  QA  +LEQ  ARW YL  +LD PL +A   LAALG E +   FE+RL  +
Sbjct: 614  RDERLGERQRQARHVLEQARARWRYLYEHLDTPLAQALPALAALGFEPLRGDFERRLERE 673

Query: 680  PEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALHM 739
            PEA +F +VQDR+VR SWK EVRA LR+ F G+ F  ++E  +AIHKRVLRGRV++ALHM
Sbjct: 674  PEARIFDLVQDRSVRTSWKTEVRAHLRRSFVGSTFAPVIEAVEAIHKRVLRGRVWIALHM 733

Query: 740  HAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTEDE 799
            HAGDGNVHTNIPVNSD YEMLQ+A+ AV RIM++ARSL GVISGEHGIGITKLEFL+  E
Sbjct: 734  HAGDGNVHTNIPVNSDDYEMLQEANRAVKRIMQIARSLGGVISGEHGIGITKLEFLSAAE 793

Query: 800  IGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIAS 859
              +FR YK R+DP+G FN+GKL+  PG   DL NAYTPSF LMGHESLIMQQSDI +IA+
Sbjct: 794  TADFRRYKNRIDPDGHFNRGKLM--PG--GDLRNAYTPSFKLMGHESLIMQQSDIASIAA 849

Query: 860  SVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEEF 919
            +VKDCLRCGKCKPVC+THVPRANLLYSPRNKILATSLL+EAFLYEEQTRRGVSI+H++EF
Sbjct: 850  AVKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLIEAFLYEEQTRRGVSIRHFDEF 909

Query: 920  EDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPAT 979
             DVA+HCT+CHKC  PCPVDIDFGDVSM MR+LLR+MGKK FN GT A+MFFLNAT P T
Sbjct: 910  ADVAEHCTLCHKCEKPCPVDIDFGDVSMAMRDLLRRMGKKRFNPGTAASMFFLNATHPET 969

Query: 980  INATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATVGKPPVKEQVIHFINKKMPGNLP 1039
            I  TRKVM +WGFKAQRL    M  FA  QT +PPAT GKPPV EQV+HF+NKKMP  LP
Sbjct: 970  IKLTRKVMLEWGFKAQRLAGRAMSVFASPQTARPPATTGKPPVHEQVVHFVNKKMPAGLP 1029

Query: 1040 KKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWNVGV 1099
            K+TARALLDIED   VPIIR+P  T++++EAVFYFPGCGSERLFSQVGLATQAMLW +GV
Sbjct: 1030 KRTARALLDIEDRNYVPIIRDPARTSSESEAVFYFPGCGSERLFSQVGLATQAMLWQIGV 1089

Query: 1100 QTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTCYDQ 1159
            QTVLPPGY+CCGYPQRG GDF K +K+ITDNRVLFHR++ TLNYLDI+TVVVSCGTCYDQ
Sbjct: 1090 QTVLPPGYMCCGYPQRGNGDFSKADKMITDNRVLFHRVSTTLNYLDIRTVVVSCGTCYDQ 1149

Query: 1160 LQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVNSLI 1219
            LQ Y+FE+IFPGCRI+DIHE+L+E+GV+L G TG RYMYHDPCH+P+K  DP++ VN+LI
Sbjct: 1150 LQDYKFEEIFPGCRIVDIHEFLMERGVRLAGATGVRYMYHDPCHTPIKTHDPMQVVNTLI 1209

Query: 1220 TTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRADGFTGDVKILT 1279
                  ++EKN+RCCGESGTF +SRPDV+TQVRFRKEEEMR G+ K+RADGF G+VKILT
Sbjct: 1210 NEQVNGRVEKNERCCGESGTFAISRPDVATQVRFRKEEEMRAGAQKLRADGFQGEVKILT 1269

Query: 1280 SCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333
            SCPSC QGL RYN+DA T ADYIV+E+ARH+LGE W+PEYV+ AN GGIER+LV
Sbjct: 1270 SCPSCMQGLKRYNDDAATEADYIVIEIARHVLGERWLPEYVKAANAGGIERVLV 1323


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: 4235
Number of extensions: 159
Number of successful extensions: 4
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: 1323
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1274
Effective search space:  1635816
Effective search space used:  1635816
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 Jul 25 2024. The underlying query database was built on Jul 25 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