GapMind for Amino acid biosynthesis

 

Alignments 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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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:

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:

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:

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:

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