Alignments for a candidate for serA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_018233617.1 THITHI_RS0113380 FAD-linked oxidase

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



>NCBI__GCF_000378965.1:WP_018233617.1
          Length = 1289

 Score = 1503 bits (3890), Expect = 0.0
 Identities = 770/1321 (58%), Positives = 962/1321 (72%), Gaps = 54/1321 (4%)

Query: 22   RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81
            R+REIPYNYTSFSDREIVIR LGE  W +L+ELRG+R+TG SARML+EVLGD+WVV RNP
Sbjct: 14   RIREIPYNYTSFSDREIVIRFLGEAMWEVLNELRGERRTGVSARMLFEVLGDMWVVTRNP 73

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            Y+QDDLLDN KR  ALI A++HRL ++  R    + A                L   A++
Sbjct: 74   YIQDDLLDNRKRLTALIGAMDHRLDQIVARADGNENALE--------------LAARARE 119

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+  F + F +   LR+R  + L R T +DNI FDGL+RVSHVTDATDWRVE PFVV+TP
Sbjct: 120  AVRRFEDWFPEHKALRRRTLRKLSRHTRRDNIHFDGLARVSHVTDATDWRVELPFVVITP 179

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            D+E EMAG+V ACI LGLT+IPRGGGTGYTG A+PL   SAVINTEKLE LG VE+  +P
Sbjct: 180  DSEAEMAGVVDACIRLGLTVIPRGGGTGYTGAAVPLDARSAVINTEKLEGLGEVEIRRIP 239

Query: 262  GLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWG 321
            G+  P  T+ + AGVVT+RV+D A + GF FAVDPTS +AS IGGN+AMNAGGKKAVLWG
Sbjct: 240  GVAAPVPTVRAEAGVVTRRVADLAGREGFAFAVDPTSQDASTIGGNIAMNAGGKKAVLWG 299

Query: 322  TALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKTEI 381
            T +DNL SWRMV P   WLEV R+ HNLGKIHD E  RF++           T   + E 
Sbjct: 300  TTIDNLVSWRMVTPDAGWLEVERIGHNLGKIHDQETVRFRIT---RFRSDGATPAGEPEE 356

Query: 382  LEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFFG 441
            +   G  FR+ GLGKDVTDK L GLPG+QKEGCDGLITSA ++LH+MP+  RTVCLEF+G
Sbjct: 357  ISCPGSTFRRLGLGKDVTDKHLGGLPGIQKEGCDGLITSAVFVLHRMPRHVRTVCLEFYG 416

Query: 442  -QARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLIG 500
                +A+P+IVEIKD LDA+ +     L+GLEHLDERY+RAV Y  K  RG  PKMVL+ 
Sbjct: 417  HDLHEAVPAIVEIKDRLDADPR---VKLSGLEHLDERYVRAVRYTPKGARGERPKMVLLA 473

Query: 501  DIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKIN 560
            D+  DDE AV  AASEV+R+AN R GEGFVAVSPEARK+FW +R+RTAAIA HTNAFKIN
Sbjct: 474  DVSSDDEEAVGRAASEVVRLANARNGEGFVAVSPEARKRFWSERARTAAIAAHTNAFKIN 533

Query: 561  EDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLP-LGKSDDAEGDDIP 619
            EDVVIPL+R+ EY++GIERINI  S+ NKL+++AE     +KG+ P L +    E ++  
Sbjct: 534  EDVVIPLDRLAEYSEGIERINIVQSMNNKLRMVAETLE-CLKGDHPELRQLLAIENEE-- 590

Query: 620  AAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVD- 678
            A    E +   A   LE   ARW  +L NLD    +A  + A L         + R  D 
Sbjct: 591  ARRWFEGKRRAATRHLEGVQARWKLILGNLD---ADAVSQDALL---------DDRARDD 638

Query: 679  -QPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVAL 737
             +P   V  ++  R++RIS+K+EVR  L  IF G   + + +  +AIH RVL  R+FVAL
Sbjct: 639  LRPGDRVIDLLLRRSLRISYKREVRRPLWDIFDGLELEPVRKRLEAIHDRVLTSRLFVAL 698

Query: 738  HMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTE 797
            HMHAGDGNVHTNIPVNS+ Y M+ +A   V ++M LAR L GVISGEHGIGITK+++L  
Sbjct: 699  HMHAGDGNVHTNIPVNSNDYAMMHEAERIVDQVMALARRLGGVISGEHGIGITKMQYLEP 758

Query: 798  DEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAI 857
             ++  F  YK+RVDP+G FN+GKL  +PG  + L+NAYTPS  L+  E+LI++QS++GA+
Sbjct: 759  GQVEAFAGYKQRVDPQGHFNRGKL--MPG--SGLANAYTPSLRLLQQEALILEQSELGAL 814

Query: 858  ASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWE 917
               +KDCLRCGKCKPVC+THVPRANLLYSPRNKILA+ L++EAFLYEEQTRRG+S++H++
Sbjct: 815  NEDIKDCLRCGKCKPVCNTHVPRANLLYSPRNKILASGLIIEAFLYEEQTRRGLSLRHFD 874

Query: 918  EFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDP 977
            E  DVADHCT+CHKC  PCPV+IDFGDV++ MR++L++ G++     T A+M FLN  DP
Sbjct: 875  EMNDVADHCTICHKCEPPCPVNIDFGDVTIRMRSILKERGRRRVKLVTRASMAFLNIKDP 934

Query: 978  ATINATRKVMTQWGFKAQRLGNDLMKKFA-KKQTQKPPATVGKPPVKEQVIHFINKKMPG 1036
            ATI   R+ M QWG+ AQRLG  L ++      +Q+P +T  +  +  QV+ F+ K MP 
Sbjct: 935  ATIKLMRRGMVQWGYAAQRLGYGLFRRLGLLGGSQRPASTASRASLPAQVVQFVKKPMPA 994

Query: 1037 NLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWN 1096
             LP +T RA+L +ED  +VP+IR+P       +AVFYFPGCGSERLFSQVGLAT AML++
Sbjct: 995  GLPARTTRAMLGLEDAGLVPVIRDPAKAGEQGDAVFYFPGCGSERLFSQVGLATIAMLYD 1054

Query: 1097 VGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTC 1156
            VG QTVLPPGYLCCGYPQ   GD +KG  I T+NRVLFHR+ANTLNYLDI+TV+VSCGTC
Sbjct: 1055 VGAQTVLPPGYLCCGYPQTSAGDVDKGRAITTENRVLFHRVANTLNYLDIRTVIVSCGTC 1114

Query: 1157 YDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVN 1216
             DQL  YEFE+IFPGCR++DIHEYL+EKG+ LEGV G +Y+YHDPCHSPMK   P +  +
Sbjct: 1115 MDQLLKYEFERIFPGCRLLDIHEYLMEKGLSLEGVKGVQYLYHDPCHSPMKTHAPGQVAS 1174

Query: 1217 SLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKG----SDKVRADGFT 1272
             L+     Q++  +DRCCGE+GTF VSRPD++TQVRFRKEEE+R G    + + +A+G  
Sbjct: 1175 RLM----GQEVRISDRCCGEAGTFAVSRPDIATQVRFRKEEELRAGIRELTGRDQAEG-- 1228

Query: 1273 GDVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERIL 1332
            GDVK+LTSCP+C QGLSRY ED G   DYIVVEMA  LLGE W   ++ERA +GGIE++L
Sbjct: 1229 GDVKMLTSCPACQQGLSRYREDTGLETDYIVVEMANRLLGEGWQERFIERARSGGIEKVL 1288

Query: 1333 V 1333
            +
Sbjct: 1289 L 1289


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: 4112
Number of extensions: 168
Number of successful extensions: 12
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: 1289
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1241
Effective search space:  1594685
Effective search space used:  1594685
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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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