Aligments for a candidate for serA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Aligments for a candidate for serA in Cupriavidus basilensis 4G11

Align Phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate RR42_RS02380 RR42_RS02380 FAD-linked oxidase

Query= reanno::BFirm:BPHYT_RS03150
         (1364 letters)



>FitnessBrowser__Cup4G11:RR42_RS02380
          Length = 1324

 Score = 2237 bits (5796), Expect = 0.0
 Identities = 1101/1365 (80%), Positives = 1198/1365 (87%), Gaps = 42/1365 (3%)

Query: 1    MNAPQVFDPHGAAATVAADPEARLREIPYNYTSFSDREIVIRLLGDEAWAVLAELRAERR 60
            MNAP V D    A   A D  ARLREIPYNYTSFSDREIVIRLLG+EAW +LAELR ERR
Sbjct: 1    MNAPLVLD----AKLAAQDAPARLREIPYNYTSFSDREIVIRLLGEEAWRILAELRGERR 56

Query: 61   TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAMLIEALHHRLSEIEKRRRADLTEH 120
            TGRSARMLYEVLGDIWVVRRNPYLQDDLL+NPKRR ML+ ALHHRLSE+EKRR AD  EH
Sbjct: 57   TGRSARMLYEVLGDIWVVRRNPYLQDDLLENPKRRQMLVTALHHRLSEVEKRRAADRAEH 116

Query: 121  GDEAGVDRAARVETLVQAARRAVDEFASEFQKTYDLRKRATKVLGKVTEKDNIKFDGLSR 180
             + A  DR+ RVE LV  A++A+++F  EF   YDLRKR  +VLG++T+KDNIKFDGLSR
Sbjct: 117  AEPAAEDRSHRVEQLVSFAKQAIEDFKQEFAHAYDLRKRTQRVLGRITQKDNIKFDGLSR 176

Query: 181  VSHVTDATDWRVEYPFVVLTPDTEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF 240
            VSHVTDATDWRVEYPFVVLTPDTE EIAGM+K CFELGLT+IPRGGGTGYTGGAVPLTP 
Sbjct: 177  VSHVTDATDWRVEYPFVVLTPDTEEEIAGMVKGCFELGLTIIPRGGGTGYTGGAVPLTPM 236

Query: 241  SAVINTEKLEQLGAVEMTELPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD 300
            SAVINTEKLEQLG VE T+LPGV  KV TIFSGAGVVTRRV +AA++AG VFAVDPTS+D
Sbjct: 237  SAVINTEKLEQLGPVEQTDLPGVSHKVGTIFSGAGVVTRRVADAADKAGLVFAVDPTSID 296

Query: 301  ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNMGKIHDIEVARF 360
            ASC+GGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHN+GKIHD+ VA F
Sbjct: 297  ASCIGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNLGKIHDVAVATF 356

Query: 361  RLDWFDGNYAPGEKLMRTEALDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA 420
             L W DGN APGEK +RTE L I+GR FRKEGLGKDVTDKFLAGLPG+QKEGCDG+ITSA
Sbjct: 357  ELKWSDGNRAPGEKPLRTETLAIEGRKFRKEGLGKDVTDKFLAGLPGIQKEGCDGIITSA 416

Query: 421  RWVLHKMPAHTRTVCLEFFGQARDAIPSIVEIKDYL-FETSKQGGAILAGLEHLDERYLR 479
            RW+LH+MPAH RTVCLEFFGQARDAIPSIVEIKDYL  E+   GGAILAGLEHLDERYLR
Sbjct: 417  RWILHRMPAHVRTVCLEFFGQARDAIPSIVEIKDYLDAESRTPGGAILAGLEHLDERYLR 476

Query: 480  AVGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVNAEARKRF 539
            AVGYATKSKRNAFPKMVLIGDIVGDD DAVA+ATSEV+RMANGKSGEGFVAV+ EARK+F
Sbjct: 477  AVGYATKSKRNAFPKMVLIGDIVGDDQDAVARATSEVIRMANGKSGEGFVAVSPEARKKF 536

Query: 540  WLDRSRTAAIAKHTNAFKINEDVVIPLDRMGEYTDGIERINIELSIKNKLQLVDALEAFF 599
            WLDRSRTAAIA+HTNAFKINEDVVIPL RMGEYTDGIERINIELSIKNKLQL DALEAFF
Sbjct: 537  WLDRSRTAAIARHTNAFKINEDVVIPLPRMGEYTDGIERINIELSIKNKLQLTDALEAFF 596

Query: 600  KGGKLPLGKSDDANEIPSAELLEDRVQQALDLLKRVRTRWEFLRDKLDLSLREAQHYLVG 659
              G LPLG+SDDANEIPSAELLEDRVQ AL LL+ +R+RW +L+D LD  L  A+  L+G
Sbjct: 597  ARGNLPLGRSDDANEIPSAELLEDRVQHALQLLREIRSRWTYLQDHLDTPLATARASLIG 656

Query: 660  LGYEAMAEKFADRVDAQPDVNVFHVTQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQ 719
             G   + + F  R++ QPD  VFH+ QDRTIRVSWK E+RAELR IFNGGEFKPILDEAQ
Sbjct: 657  HGLGLLGQAFEARLEQQPDATVFHLLQDRTIRVSWKSEVRAELRNIFNGGEFKPILDEAQ 716

Query: 720  AIHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHTAVARIMKLARSLDGVIS 779
             IHKQVLRGRVFVALHMHAGDGNVHTN+PVNSD+Y+MLQDAH AVARIM LARSLDGVIS
Sbjct: 717  KIHKQVLRGRVFVALHMHAGDGNVHTNIPVNSDDYDMLQDAHRAVARIMALARSLDGVIS 776

Query: 780  GEHGIGITKLEFLTEDEISEFRQYKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYES 839
            GEHGIGITKLEFLTEDEI EFR+YKQRVDP GRFN GKLL GADLRNAYTPSFGLMG+ES
Sbjct: 777  GEHGIGITKLEFLTEDEIGEFREYKQRVDPQGRFNKGKLLPGADLRNAYTPSFGLMGHES 836

Query: 840  LIMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQ 899
            +IMQQSDIGAI++S+KDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQ
Sbjct: 837  IIMQQSDIGAIADSVKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQ 896

Query: 900  TRRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDVTMNMRNLLRKMGKKKFNPGNA 959
            TRRG+SIKHWDEF+DVADHCTVCHKCVTPCPVKIDFGDV+MNMRNLLRKMG+KKFNPG A
Sbjct: 897  TRRGISIKHWDEFSDVADHCTVCHKCVTPCPVKIDFGDVSMNMRNLLRKMGQKKFNPGTA 956

Query: 960  AGMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKPPVTQQV 1019
            A MFFLNATNPQTIN+ R  M+  GYKAQRLGN+VLKKF +KQTAHPPATVG+ PV +QV
Sbjct: 957  ASMFFLNATNPQTINMTRKVMIDWGYKAQRLGNDVLKKFARKQTAHPPATVGRAPVQEQV 1016

Query: 1020 IHFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQV 1079
            IHF+NKKMPGNLPKKTARALLDIEDN+IVPIIR+PK T+ +TEAVFYFPGCGSERLFSQV
Sbjct: 1017 IHFINKKMPGNLPKKTARALLDIEDNEIVPIIRDPKRTSPETEAVFYFPGCGSERLFSQV 1076

Query: 1080 GLATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQFDKAEQIVTDNRVLFHRVANTLNYLDI 1139
            GLATQAMLW  GVQTVLPPGYLCCGYPQRG+GQFDKAE++VTDNRVLFHRVANTLNYLDI
Sbjct: 1077 GLATQAMLWHVGVQTVLPPGYLCCGYPQRGNGQFDKAEKMVTDNRVLFHRVANTLNYLDI 1136

Query: 1140 KTVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHEFLLEKGMKLDGVNGVRYMYHDPCHTPI 1199
            KTVVVSCGTCYDQLAGYEF+KIFPGCRIIDIHE+LLEKG+KL+GV G RYMYHDPCHTPI
Sbjct: 1137 KTVVVSCGTCYDQLAGYEFDKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHTPI 1196

Query: 1200 KTMDPIKLVNQLMGSEKDGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAK 1259
            KTMDP KLVN+LMG  + G KIEKN+RCCGESGTLAV+RPD+STQ+RFRKEEE+ KGA K
Sbjct: 1197 KTMDPTKLVNELMGGNEGGSKIEKNERCCGESGTLAVSRPDVSTQIRFRKEEEMTKGADK 1256

Query: 1260 LRGIPLVAEAGANGINPANASAGSAGAPEGSVLKAGDGPQPKGATDVKILTSCPSCLQGL 1319
            LR                  + G  G                   DVKILTSCPSCLQGL
Sbjct: 1257 LR------------------TDGFVG-------------------DVKILTSCPSCLQGL 1279

Query: 1320 SRYNEDAGIEADYIVVEMARHVLGEDWMVDYVQRANNGGIERVLV 1364
            SRY EDA + ADYIVVEMA+H+LGE+WM DYV +AN+GGIERVLV
Sbjct: 1280 SRYKEDATVTADYIVVEMAKHLLGENWMPDYVAKANSGGIERVLV 1324


Lambda     K      H
   0.320    0.136    0.406 

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: 4578
Number of extensions: 159
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1364
Length of database: 1324
Length adjustment: 49
Effective length of query: 1315
Effective length of database: 1275
Effective search space:  1676625
Effective search space used:  1676625
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 (21.8 bits)
S2: 59 (27.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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