Alignments for a candidate for serA in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Thiomicrorhabdus chilensis DSM 12352

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_028486991.1 B076_RS0108865 FAD-linked oxidase

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



>NCBI__GCF_000483485.1:WP_028486991.1
          Length = 1286

 Score = 1409 bits (3648), Expect = 0.0
 Identities = 713/1323 (53%), Positives = 936/1323 (70%), Gaps = 55/1323 (4%)

Query: 22   RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81
            R+REIPYNYTSFSD+EIV+R LGE  W  ++ LR  R TGRSARML+EVLGD+WVV RNP
Sbjct: 8    RIREIPYNYTSFSDKEIVLRFLGESGWRTIESLRDSRNTGRSARMLFEVLGDMWVVTRNP 67

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            Y+QDDL++NPKRR AL++ALNHRL +V++R    + AE               LL + + 
Sbjct: 68   YIQDDLIENPKRRDALVKALNHRLKQVEQRLNGNELAED--------------LLLSVRD 113

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+  F+E F +  +LR +  K L +FT  DNI F GL+RVSH TDATDWRVE P VV++P
Sbjct: 114  AVISFSEWFPRQIELRSQVKKKLSKFTRNDNIDFGGLARVSHATDATDWRVELPLVVVSP 173

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            D E+E+A +V ACIELGLT+IPRGGGTGYTGGAIPL   S VINTEKLE +  VE   LP
Sbjct: 174  DKEEEIAYIVNACIELGLTMIPRGGGTGYTGGAIPLHQDSVVINTEKLEYMSLVEQAELP 233

Query: 262  GLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWG 321
            G+ K   TI +GAGVVT+RVS+ AE+ G+VFAVDPTS +ASCIGGN+AMNAGGKKAVLWG
Sbjct: 234  GIGK-VPTIQTGAGVVTRRVSEQAERFGYVFAVDPTSQDASCIGGNIAMNAGGKKAVLWG 292

Query: 322  TALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKTEI 381
            T LDNLASW+MV P   WLE++R++HNLGK+ D ++  F+++     E    T++     
Sbjct: 293  TTLDNLASWKMVMPDATWLEISRINHNLGKLQDQKLVSFEMQRY---EMDGVTKIDSPVR 349

Query: 382  LEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFFG 441
            L++ G  FRK GLGKDVTDKFLSGLPGVQKEGCDG+ITSAR+++H+MP  TRTVCLEFFG
Sbjct: 350  LDMPGSAFRKAGLGKDVTDKFLSGLPGVQKEGCDGIITSARFVVHRMPSHTRTVCLEFFG 409

Query: 442  QARD-AIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLIG 500
                 A+P+IVEI D+++++ K+ G +LAGLEHLDERY++AV Y TK+ R  LPKM+L+ 
Sbjct: 410  TDLSLAVPAIVEITDFIESK-KQQGILLAGLEHLDERYIKAVKYNTKANRKGLPKMILLA 468

Query: 501  DIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKIN 560
            DI G++   VA   SE++ +AN R  EGF+AVS EARK+FW DRSRTAAI+ HTNAFKIN
Sbjct: 469  DICGENGFEVANTCSEIVELANKRDAEGFIAVSEEARKRFWSDRSRTAAISAHTNAFKIN 528

Query: 561  EDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAEGDDIPA 620
            EDVVIPL R+ +Y + IERINIELSI+NKL +L  L  +F        + DD E    P 
Sbjct: 529  EDVVIPLERLNDYNNEIERINIELSIQNKLDILDSLSDYFSSPIKEFSQEDDFEDSKGPT 588

Query: 621  AEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVDQP 680
            +   + +V   +S L Q   RWS +LA+LD P             E+ L ++   + D+ 
Sbjct: 589  S-YFKGKVEATKSHLSQVKQRWSSILAHLDTPA------------EQHLNLYPAGVADKV 635

Query: 681  EAA--VFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALH 738
                 V +++  R + +S++QEV   L++ F G  F+ + ++ + +H  +   R+FVALH
Sbjct: 636  REGDQVINLLLRRDLTVSYRQEVLEFLKETFMGHDFEPLHKKLKELHFELRNARLFVALH 695

Query: 739  MHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTED 798
            MHAGDGN+HTNIPV+S++YEM+  A   V RIM +A  L GVISGEHGIG+TK ++L  D
Sbjct: 696  MHAGDGNIHTNIPVHSNNYEMIHLADKVVDRIMDIAHRLGGVISGEHGIGLTKFQYLEAD 755

Query: 799  EIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIA 858
            +I +F +YK+++DP+G FN+GKL+  PG  + L  AYTPS  L+  E+LI++ +++  + 
Sbjct: 756  KIADFVQYKQKIDPQGHFNRGKLM--PG--SGLQKAYTPSLQLVQQEALILEATELDELN 811

Query: 859  SSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEE 918
            + +KDCLRCGKCKPVC TH+PRANLLYSPRNKILAT  ++EAFLYEEQTRRG+S+ H++ 
Sbjct: 812  NDIKDCLRCGKCKPVCQTHIPRANLLYSPRNKILATGQVIEAFLYEEQTRRGISLHHFDA 871

Query: 919  FEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPA 978
              DVADHCT CHKC  PCPVDIDFGDVS+ MR +L  MG+K  +    AA+ FLN  +P 
Sbjct: 872  MNDVADHCTTCHKCEAPCPVDIDFGDVSIRMRTILTNMGQKKNSLMVKAALLFLNTKNPM 931

Query: 979  TINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKP-PATVGKPP-VKEQVIHFINKKMPG 1036
            TI   RK M  WG  A  LG+ L K       +K  PA+  +P  V+ QVI+F+ K +  
Sbjct: 932  TIKVLRKTMIGWGSIAITLGHKLAKWTGLVGRKKVLPASSSQPASVQLQVINFVRKPLDT 991

Query: 1037 NLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWN 1096
               + + R +L +ED   +PI+R+P  TT D+EAVFYFPGCGSERLFS +GLAT + L++
Sbjct: 992  GPNQSSYRNVLGLEDATQIPIVRDPAKTTEDSEAVFYFPGCGSERLFSDIGLATISSLYD 1051

Query: 1097 VGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTC 1156
             GVQT+LPPGYLCCGYPQ   G  +   +I T+NR LFHR+ANTLNY+DIKTV+VSCGTC
Sbjct: 1052 AGVQTILPPGYLCCGYPQAAAGLAQTSSQITTENRALFHRVANTLNYMDIKTVIVSCGTC 1111

Query: 1157 YDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVN 1216
            YDQL  YEFE+IFPGCR++DIHE+L EKG+ LEG TG +Y+YH PCH PMKQ D  +   
Sbjct: 1112 YDQLTKYEFERIFPGCRLLDIHEFLTEKGMGLEGATGKQYLYHAPCHDPMKQMDGTQVAK 1171

Query: 1217 SLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRK------GSDKVRADG 1270
             L+ +    +++ +DRCC E+GT   +RPD++ Q+RFRKE E+++      G DK+    
Sbjct: 1172 DLLQS----EVQFSDRCCSEAGTMATARPDIARQLRFRKEAELKQGLIDLTGKDKIS--- 1224

Query: 1271 FTGDVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIER 1330
              G VK+LTSCP+C QGL RY ++ G   DYIVVE+ ++  G+ W  E++ +   GGIE+
Sbjct: 1225 -DGSVKVLTSCPACQQGLGRYADNTGMDTDYIVVELMKNRYGDKWNKEFLAKLEAGGIEK 1283

Query: 1331 ILV 1333
            +L+
Sbjct: 1284 VLL 1286


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: 3876
Number of extensions: 151
Number of successful extensions: 13
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: 1286
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1238
Effective search space:  1590830
Effective search space used:  1590830
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)
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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