GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Dinoroseobacter shibae DFL-12

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 3608920 Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= reanno::Marino:GFF2744
         (1209 letters)



>lcl|FitnessBrowser__Dino:3608920 Dshi_2311
            delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
          Length = 1221

 Score = 1263 bits (3267), Expect = 0.0
 Identities = 665/1209 (55%), Positives = 848/1209 (70%), Gaps = 19/1209 (1%)

Query: 15   RQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRKNAKSTIMEKFLAEY 74
            R  +R +Y A+E  ++  + A  +LS  ER+  +A  A  V  VR   + ++ME FLAEY
Sbjct: 16   RAQVRAHYTAEETALLKSLAARIKLSAHEREKAAAAGARYVTRVRNETRPSMMEAFLAEY 75

Query: 75   GLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKASSGLINTATVALLM 134
            GL+T EGV LMCLAEALLRVPD  TI +LIEDK+    WG H+G +SS L+N +T AL++
Sbjct: 76   GLSTSEGVGLMCLAEALLRVPDADTIDDLIEDKVAPSNWGAHLGHSSSSLVNASTWALML 135

Query: 135  TSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEAQDEAKEY 194
            T  +L +  R      LR L+KR GEPV+RT  GQ+MK +GRQFVLG+ I+E    A+E 
Sbjct: 136  TGKVLDEDPRGPA-RALRGLVKRLGEPVVRTAVGQSMKVLGRQFVLGQTIEEGLKNAREL 194

Query: 195  MAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRKNPGISVKLSALLAR 254
              KG+TYSYDMLGEAARTD DA+RY+ +Y+ AI +IA+ + GDVR +PGISVKLSAL  R
Sbjct: 195  EKKGFTYSYDMLGEAARTDADARRYHAAYAQAITAIARQATGDVRSSPGISVKLSALHPR 254

Query: 255  YEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLDVIEELVADPELAGW 314
            YEY ++  VM +L+PRA  LVK+AA A +GFN+DAEEQDRLDLSLDVIE +++DP+L GW
Sbjct: 255  YEYTHRHSVMADLVPRAAALVKQAAQAGIGFNVDAEEQDRLDLSLDVIEAMMSDPDLDGW 314

Query: 315  DGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVMGLNGFPVF 374
            DGFGVVVQAYG+R+  V++ LY +AE+YDRK MVRLVKGAYWD EIK AQ +G+  FPVF
Sbjct: 315  DGFGVVVQAYGRRAGPVIETLYDMAERYDRKIMVRLVKGAYWDTEIKLAQELGVERFPVF 374

Query: 375  TRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTKGVDNYEFQRLHGMG 434
            TRK  +DVS+++CA  LL+  +RIYPQFATHNAH+ +A+L+MA     D +EFQRLHGMG
Sbjct: 375  TRKNNTDVSYMACAQMLLDRRDRIYPQFATHNAHTCAAVLQMAGNAR-DCFEFQRLHGMG 433

Query: 435  ESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVNQIVDKRITPEEIAK 494
             SLH  V +  G  CRIYAPVG H+DLLAYLVRRLLENGANSSFVNQIVD  I  E I+ 
Sbjct: 434  ASLHQIVKETEGTRCRIYAPVGAHQDLLAYLVRRLLENGANSSFVNQIVDPDIPAEAISA 493

Query: 495  DPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEIEKGRGAYKDYRWKG 554
            DP+  +E++G+ I + AI  P  LF   RRNS+G+ + +P ++  +   R A+ +  W  
Sbjct: 494  DPVSEMEKLGDQIPNPAIRQPSDLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHA 553

Query: 555  GPLIAGEVAGT-EIQVVRNPADPDDLVGHVTQASDADVDTAITSAAAAFESWSAKSAEER 613
             P++AG    T   + V +PAD   LVG V +AS  DV  A+ +A   F  WSA+   ER
Sbjct: 554  RPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAEDVACALDAAETGFRDWSARPVSER 613

Query: 614  AACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEAIRYK--DSG 671
            A  +RK+ D+YE+N AEL A+TTREAGK++LD +AE+REAVDF ++YANEA R +  D G
Sbjct: 614  ADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAERLEEEDPG 673

Query: 672  DARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELMHQAGIPKD 731
              RG+  CISPWNFPLAIFTGQI A L  GN V+AKPAEQT ++A RAV++M   G+P  
Sbjct: 674  RPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDA 733

Query: 732  AIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLVAETGGLNA 791
            A+QL+PG G  VG  LTSD R++GVCFTGST  A  I+K + +N  P+A LVAETGGLNA
Sbjct: 734  ALQLLPGDGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNA 793

Query: 792  MIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLYGAMEELGIGDP 851
            MIVDSTAL EQ VRD+L SSFQSAGQRCSALR+LYVQ D+ D L+EML GA++ L IGD 
Sbjct: 794  MIVDSTALHEQAVRDILISSFQSAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDS 853

Query: 852  WLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAVLSVSGIEELEE 911
            W L  DV PVID +A+  I+ + ++  + G L+K +  P+ G +V+PA++ V GI ++E 
Sbjct: 854  WNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLAAPDSGTYVTPAIVKVGGIADMER 913

Query: 912  EIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKVGNTYVNRN 971
            EIFGPVLHVATF+A  ID+VVD INA+ YGLTFG+H+R+D RVE+I  RI+VGN YVNRN
Sbjct: 914  EIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIVERIQVGNVYVNRN 973

Query: 972  QIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLK-GETVEREADSNARKVDAKQLQKLIG 1030
            QIGAIVGSQPFGGEGLSGTGPKAGGP Y+ RF K G++    A   A  +    L   + 
Sbjct: 974  QIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKVGKSTSHPAPQGA-VLGKAALNTALS 1032

Query: 1031 QLDKLK-ASRPE----ARMDAIRPIFGNVPEPL------DAHVEALPGPTGETNRLSNHA 1079
             LD    A+RP+     RM A+    G V   L      D   + LPGPTGE+NRLS   
Sbjct: 1033 SLDARNWAARPDRVHILRM-ALSGSTGVVRRALSETAAFDMSPQTLPGPTGESNRLSMVP 1091

Query: 1080 RGVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEA 1139
            RG VLCLGP  E A+ QA  AL  G  VV+  PG+  +    + AG P+V   G ++   
Sbjct: 1092 RGTVLCLGPTPEIAMAQAVQALGAGCAVVIALPGSTPLSQPLSDAGAPVVTLDGTVDCVT 1151

Query: 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAG 1199
            L  + G E V + G     +  R AL++RDG ++PLI +    +R+V+ERHLC+DTTAAG
Sbjct: 1152 LTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVDEIAPERYVLERHLCIDTTAAG 1211

Query: 1200 GNASLIAAS 1208
            GNA L+AAS
Sbjct: 1212 GNAKLLAAS 1220


Lambda     K      H
   0.316    0.133    0.378 

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: 3465
Number of extensions: 168
Number of successful extensions: 6
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: 1209
Length of database: 1221
Length adjustment: 47
Effective length of query: 1162
Effective length of database: 1174
Effective search space:  1364188
Effective search space used:  1364188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (27.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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