Alignments for a candidate for serA in Thiomicrospira microaerophila ASL8-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Thiomicrospira microaerophila ASL8-2

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_044410013.1 NA59_RS06820 FAD-linked oxidase

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



>NCBI__GCF_000934765.1:WP_044410013.1
          Length = 1286

 Score = 1446 bits (3742), Expect = 0.0
 Identities = 732/1325 (55%), Positives = 935/1325 (70%), Gaps = 51/1325 (3%)

Query: 19   TPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVR 78
            T  R+REIPYNYTSFSDREIV R +GE  W  +++LR  R TGRSA+ML+EVLGD+WVV 
Sbjct: 3    TNKRIREIPYNYTSFSDREIVTRFIGESGWQTVEQLRESRGTGRSAQMLFEVLGDMWVVT 62

Query: 79   RNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKA 138
            RNPY+QDDLL+N KRRAAL EAL+HRL +V+ R                 +   E+LL A
Sbjct: 63   RNPYIQDDLLENAKRRAALTEALHHRLSQVESRL--------------NNNKLAESLLNA 108

Query: 139  AKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVV 198
             ++A+  F + F     LR++ +K L + T  DN+ F GL+RVSH TDATDWRVE P VV
Sbjct: 109  VRQAVKQFEDWFPAQITLRQKVSKRLKKITRLDNVDFGGLARVSHATDATDWRVELPLVV 168

Query: 199  LTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEME 258
            + PDTE E A +V ACIELGL IIPRGGGTGYTGGAIPL   +AVINTEKLE L  VE  
Sbjct: 169  ICPDTEQETADIVAACIELGLIIIPRGGGTGYTGGAIPLDANTAVINTEKLEFLSLVEKV 228

Query: 259  ILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAV 318
             LPG+     T+ +GAGVVTKRV++ AE+ G VFAVDPTS +AS IGGN++MNAGGKKAV
Sbjct: 229  ELPGVGVKVPTVRTGAGVVTKRVTELAERNGLVFAVDPTSHDASTIGGNISMNAGGKKAV 288

Query: 319  LWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFK 378
            LWGT LDNLASW+MV P   W+EV R++HNLGK+ D     F+L   H  E   KT   +
Sbjct: 289  LWGTTLDNLASWKMVMPDASWMEVVRVNHNLGKLQDQATVSFEL---HRYESDGKTPKGE 345

Query: 379  TEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLE 438
             E L+I G  FR+ GLGKDVTDKFLSGLPGVQKEGCDGLITSAR++LH+MP+  RTVCLE
Sbjct: 346  VERLDIPGSAFRQAGLGKDVTDKFLSGLPGVQKEGCDGLITSARFVLHRMPEHIRTVCLE 405

Query: 439  FFGQARD-AIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMV 497
            FFG     A+P+IVEI D+++++ K  G +LAGLEHLDERY+RAV Y TK+ R  LPKM+
Sbjct: 406  FFGTDLSLAVPAIVEITDFIESK-KAEGILLAGLEHLDERYVRAVKYNTKANRRELPKMI 464

Query: 498  LIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAF 557
            LIGDI GD+   VA    E++ +A  R  EGFVAV+ EARK+FWLDRSRTAAI+ HTNAF
Sbjct: 465  LIGDIAGDNGFEVAKTCQEIVELAKKRNAEGFVAVTAEARKRFWLDRSRTAAISAHTNAF 524

Query: 558  KINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFF---VKGNLPLGKSDDAE 614
            KINEDVVIPL R+ EY +GIERINIE+S++NK++++  L+ +F   +K    +   +D++
Sbjct: 525  KINEDVVIPLPRLNEYNEGIERINIEMSMQNKIEIIDALEDYFKAEIKEYTLVDDFEDSQ 584

Query: 615  GDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQ 674
            GD  PAA   + +V    + L Q   +W  L   LD+P             E+ L + ++
Sbjct: 585  GD--PAA-YFKSKVDTTLAHLAQVKRKWQNLYNGLDQP------------AEQFLDLLDE 629

Query: 675  --RLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGR 732
              R   + + A+  ++  R + IS+++EV   L+Q F G  F+ +++  + +H  V   R
Sbjct: 630  AARTEIRGQEALVKLILRRDLVISYRREVLDFLKQTFMGHDFEPMMKRLKELHYEVRNAR 689

Query: 733  VFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKL 792
            +FVALHMHAGDGN+HTNIPV+S++Y M+  A   V R+MKLA  L GVISGEHGIG+TK+
Sbjct: 690  LFVALHMHAGDGNIHTNIPVHSNNYRMIHQAETIVERVMKLATDLGGVISGEHGIGLTKI 749

Query: 793  EFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQS 852
            EFL+ ++I  F EYK +VDP G FNKGKL  +PG  + L NAYTPS  L+  E+LI++ S
Sbjct: 750  EFLSPEKIQAFVEYKNKVDPNGHFNKGKL--MPG--SGLHNAYTPSLSLVKQEALILEAS 805

Query: 853  DIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVS 912
            ++  + + +KDCLRCGKCKPVC TH+PRANLLYSPRNKILAT  ++EAFLYEEQTRRG+S
Sbjct: 806  ELDQLNNDIKDCLRCGKCKPVCQTHIPRANLLYSPRNKILATGQMIEAFLYEEQTRRGIS 865

Query: 913  IKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFL 972
            + H++   DVADHCT CHKC  PCPVDIDFGDVS+ MR +L  MGKK  + GT AA+F+L
Sbjct: 866  MHHFDAMNDVADHCTTCHKCEAPCPVDIDFGDVSIRMRKILTDMGKKKVSLGTKAALFYL 925

Query: 973  NATDPATINATRKVMTQWGFKAQRLGNDLMK--KFAKKQTQKPPATVGKPPVKEQVIHFI 1030
            N   P  +   R  M  WG   QR+G+ L K       + Q P  + G  PV +QVIHF+
Sbjct: 926  NTGQPGLVKLLRTTMIGWGALGQRMGHKLAKWTGILGSKDQLPAKSTGNTPVTQQVIHFV 985

Query: 1031 NKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLAT 1090
             K +     + T R+LL +ED  IVPI+R+PK TT ++EAVFYFPGCGSERLFS + LAT
Sbjct: 986  RKPLDTGPNQPTMRSLLKLEDRTIVPILRDPKKTTEESEAVFYFPGCGSERLFSDISLAT 1045

Query: 1091 QAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVV 1150
             AML+  G QT+LPPGYLCCGYPQ   G   KG +I T+NR LFHR+ANTLNY+DIKTV+
Sbjct: 1046 LAMLYETGAQTILPPGYLCCGYPQTAAGQAAKGSQITTENRALFHRVANTLNYMDIKTVL 1105

Query: 1151 VSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQD 1210
            VSCGTC DQL  YEFE+IFPGCR++DIHEYL+EKGVK+E   G +YMYH PCH PMK+ D
Sbjct: 1106 VSCGTCMDQLLKYEFEQIFPGCRLLDIHEYLMEKGVKMESTGGVQYMYHAPCHDPMKKYD 1165

Query: 1211 PLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRAD- 1269
              K    + +T+    +  +DRCC E+GT   +RPD++ Q+RFRKEEE++KG   +  + 
Sbjct: 1166 STK----VASTLTGINVPLSDRCCSEAGTLATARPDIANQLRFRKEEELKKGIKDLTGEE 1221

Query: 1270 -GFTGDVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGI 1328
                G+VK+LTSCP+C QGL+RY +D G   DYIVVE+A +L+G+ W  E+V +    G+
Sbjct: 1222 KAVNGNVKLLTSCPACQQGLNRYQDDTGLKTDYIVVELANNLIGKEWKNEFVAKVEKEGV 1281

Query: 1329 ERILV 1333
            ER+L+
Sbjct: 1282 ERVLL 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: 3925
Number of extensions: 151
Number of successful extensions: 11
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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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