Alignments for a candidate for serA in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Thioalkalivibrio denitrificans ALJD

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_077278677.1 B1C78_RS08235 FAD-linked oxidase

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



>NCBI__GCF_002000365.1:WP_077278677.1
          Length = 1288

 Score = 1507 bits (3901), Expect = 0.0
 Identities = 769/1317 (58%), Positives = 964/1317 (73%), Gaps = 47/1317 (3%)

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

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            Y+QDDLLDN +R  ALIEA++HRL ++  R           A+   R+     L   A++
Sbjct: 74   YIQDDLLDNRRRLTALIEAMDHRLDQIVAR-----------ADGNERALE---LAGRARE 119

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+  F + F +   LRKR  + L + T +DNI FDG +RVSHVTDATDWRVE PFVV+TP
Sbjct: 120  AVRRFEDWFPEQRALRKRTLRRLSKHTRRDNIHFDGFARVSHVTDATDWRVELPFVVVTP 179

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            D+E EMAG+V ACIELGLT+IPRGGGTGYTG A+PL   SAVINTEKLE LG+VEM  +P
Sbjct: 180  DSEAEMAGVVAACIELGLTVIPRGGGTGYTGAAVPLDERSAVINTEKLEGLGSVEMRRIP 239

Query: 262  GLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWG 321
            G+++   T+ + AGVVT+RVS+ A + G VFAVDPTS +AS IGGN+AMNAGGKKAVLWG
Sbjct: 240  GVEESVPTVRAEAGVVTRRVSERAAEEGLVFAVDPTSQDASTIGGNIAMNAGGKKAVLWG 299

Query: 322  TALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKL-EWSHPGEKGQKTEVFKTE 380
            T +DNLASWRMV P   WLEV R+ HNLGKIHD E  RF++  +S  G     T     E
Sbjct: 300  TTIDNLASWRMVTPDAKWLEVERVGHNLGKIHDQETVRFRITRYSADGV----TPEGAPE 355

Query: 381  ILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFF 440
             +   G+ FRK GLGKDVTDK L GLPGVQKEGCDGLITSA ++LH+MPK  RTVCLEF+
Sbjct: 356  EISAPGQSFRKLGLGKDVTDKHLGGLPGVQKEGCDGLITSAVFVLHRMPKHIRTVCLEFY 415

Query: 441  GQ-ARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLI 499
            G    +A+P+IVEIKD LD + +     L+GLEHLDERY+RAV Y  K  RG  PKMVL+
Sbjct: 416  GDDLHEAVPAIVEIKDRLDGDPQ---VRLSGLEHLDERYVRAVRYTPKGARGERPKMVLL 472

Query: 500  GDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKI 559
             D+  DDE+AV  AAS ++R+AN R GEGFVAVS EARK+FW +R+RTAAIA HTNAFKI
Sbjct: 473  ADVCSDDEDAVGRAASAMVRLANARNGEGFVAVSAEARKRFWSERARTAAIAAHTNAFKI 532

Query: 560  NEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLP-LGKSDDAEGDDI 618
            NEDVVIPL+R+ EY++GIERINI  SI NKL+++AE+    +KG+ P L +    E D+ 
Sbjct: 533  NEDVVIPLDRLAEYSEGIERINIVQSITNKLRMVAEMLEC-LKGDHPELRELLAIENDE- 590

Query: 619  PAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVD 678
                  E +   A   LE   ARW  +LA+LD+        L     E + P    RL++
Sbjct: 591  -GRRWFEGKRRAATQHLEGVQARWKLILAHLDEDAVAHDALLDERSRENLRP--GDRLIN 647

Query: 679  QPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALH 738
                    ++  R++RIS+++EV   L  IF G   + + +  +AIH RVL  R+FVALH
Sbjct: 648  --------LLLRRSLRISYRREVSRPLWDIFDGLELEPVRKRLEAIHDRVLTSRLFVALH 699

Query: 739  MHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTED 798
            MHAGDGNVHTNIPVNS+ Y M+ +A   V ++M LAR L GVISGEHGIGITK+++L   
Sbjct: 700  MHAGDGNVHTNIPVNSNDYAMMHEAERIVDQVMALARRLGGVISGEHGIGITKMQYLEPA 759

Query: 799  EIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIA 858
            ++  F  YK+RVDPEGRFN+GKL+  PG  + L+NAYTPS  L+  E+LI++QS++GA+ 
Sbjct: 760  QVDAFAGYKQRVDPEGRFNRGKLM--PG--SGLANAYTPSLRLVQQEALILEQSELGALN 815

Query: 859  SSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEE 918
              +KDCLRCGKCKPVCSTHVPRANLLYSPRNKILA+ L++EAFLYEEQTRRG+S++H++E
Sbjct: 816  EDIKDCLRCGKCKPVCSTHVPRANLLYSPRNKILASGLILEAFLYEEQTRRGLSLRHFDE 875

Query: 919  FEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPA 978
              DVADHCT+CHKC +PCPV+IDFGDV++ MRN+L++ G++     T A+M FLN  DPA
Sbjct: 876  MNDVADHCTICHKCESPCPVNIDFGDVTIRMRNILKQRGRRRVKPTTLASMAFLNIKDPA 935

Query: 979  TINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATVGKPPVKEQVIHFINKKMPGNL 1038
            TI   R+VM QWG+  QRLG+ L ++       +P +T G+  +  QV+HF+ K MP  L
Sbjct: 936  TIKLMRRVMVQWGYAGQRLGHALFRRLGLLNGARPASTTGRASLPAQVVHFVKKPMPPGL 995

Query: 1039 PKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWNVG 1098
            P +T RA+L +ED   VP++R+P       +AVFYFPGCGSERLFSQVGLAT AML++ G
Sbjct: 996  PARTTRAMLGLEDPSQVPVVRDPARADEPGDAVFYFPGCGSERLFSQVGLATIAMLYDTG 1055

Query: 1099 VQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTCYD 1158
             +TVLPPGYLCCGYPQ   GD +KG  I T+NRVLFHR+ANTLNYLDI+TV+VSCGTC D
Sbjct: 1056 AKTVLPPGYLCCGYPQTSAGDVDKGRAITTENRVLFHRVANTLNYLDIRTVIVSCGTCMD 1115

Query: 1159 QLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVNSL 1218
            QL  YEF +IFPGCR++DIHEYL+EKG+ L+GV G +Y+YHDPCH+PMK   P++  + L
Sbjct: 1116 QLLKYEFGQIFPGCRLLDIHEYLMEKGLSLKGVPGVQYLYHDPCHTPMKTHAPVQVASRL 1175

Query: 1219 ITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKG--SDKVRADGFTGDVK 1276
            +     Q++  +DRCCGE+GTF VSRPD++TQVRFRKEEE+R G      R +   GDVK
Sbjct: 1176 M----GQEVRLSDRCCGEAGTFAVSRPDIATQVRFRKEEELRAGIRGFTGRDEAVDGDVK 1231

Query: 1277 ILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333
            +LTSCP+C QGL+RY ED G   DYIVVEMA  LLGE W   ++ERA +GGIER+L+
Sbjct: 1232 MLTSCPACQQGLARYREDTGLDTDYIVVEMANRLLGEGWQERFIERARSGGIERVLL 1288


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: 4090
Number of extensions: 171
Number of successful extensions: 10
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: 1288
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1240
Effective search space:  1593400
Effective search space used:  1593400
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