Alignments for a candidate for gdhA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Dyella japonica UNC79MFTsu3.2

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate N515DRAFT_0489 N515DRAFT_0489 glutamate dehydrogenase

Query= BRENDA::A0A0H3C571
         (1607 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0489
          Length = 1644

 Score = 1199 bits (3103), Expect = 0.0
 Identities = 700/1579 (44%), Positives = 956/1579 (60%), Gaps = 79/1579 (5%)

Query: 30   EERDFLAQVGADWAIEDAPVLSAKAAAASLAEFFDFARTLKGDQPTVRLRSAGEAGAARD 89
            E + F++   +  A  D  + +A   A  +A   DF +  +  +  VR+ +     A R 
Sbjct: 32   EAQFFISAFFSRVAAGDLELHTASEWAGLIAGLLDFVQQRQPGRAAVRVFNPQAGHAGRS 91

Query: 90   LLEIVQPDRPFLVDSVMGEITESGFRVRAMFHPVVEI--------------DGIARSFIQ 135
            +++I   D PFLVD+V   I  +  ++ A+ HPVV+               DG   S + 
Sbjct: 92   VVQIATDDMPFLVDTV-SMIVSTRLQIHAVIHPVVKAVRDASGRLQRLGADDGAPESVMH 150

Query: 136  VHLDPVGED-RVESLLEQIRETLFDVRRAVGDFKAMRDLMHRAVAELAATPGVTSEEGRQ 194
              +D + ++  +  L  QI  +L DVR +V D+  MRD      A+L       +++  Q
Sbjct: 151  FEIDRLADEAEMAQLKTQIESSLDDVRASVNDWSRMRDQALAIAADLPNRQLPLNKDSMQ 210

Query: 195  EDLAFLRWLEDDNFVFLGARVYEYPRSSDGGYAAEEPLYEAEAS-LGVLRDSSRSVLRRA 253
            E + F+RWL DDNF FLG R YE  ++ DG    +E L   E S LG+L    RS+  R+
Sbjct: 211  EAVEFMRWLADDNFTFLGYREYEVTQA-DG----DEVLRSLEGSGLGILHKQERSMAPRS 265

Query: 254  YEPAILSKQLQRQLETGAPVVVAKSNLRSRVHRRGFMDYVGVRRYGDDGKPSGEVRFVGL 313
               ++ + +L +   T A +++ K+N RS VHR+G MDYVGV R+   GKP  E RF+GL
Sbjct: 266  LR-SMAASELPQSGSTDA-IILTKTNARSHVHRQGHMDYVGVLRFDAHGKPVAEQRFLGL 323

Query: 314  FTAEAYETPAVEVPLIRHRVARIMRRAAKAPGSHNEKRLRNILETWPRDELFQTSEDTLL 373
            F++ AY     +VPL+R RV  +M R+     S++ K LR+ILET PRDELFQ++ED L 
Sbjct: 324  FSSNAYMARPQDVPLVRQRVEAVMARSGLKRDSYSGKSLRHILETLPRDELFQSNEDELY 383

Query: 374  SMALGVLHLIDRPRVRLFARLDPFDRFASVLVYIPRERFDTEVCARAGAILADAYDGKVL 433
            + A+G+L L  R R RLF R D + RF + LV++PRERF+T V  R   +L DA  G+ +
Sbjct: 384  ATAIGILELRQRARTRLFVRRDRYGRFFTCLVFVPRERFNTSVRERIENMLRDALHGEQI 443

Query: 434  EYYPEISDAPLARAHFIIEVTPGDHPDPDLSQVEARIADTALTWEDRF-EAVVRAGGAPT 492
            +    + +A LAR H ++    GDH   D + +E  +A     W D   +A+V+  G   
Sbjct: 444  DSSVLMGEAALARLHIVVRPRIGDHVSYDAAALEQSVAAIVRNWHDDLRDALVKLMGDHD 503

Query: 493  GGVRTLLDKYGYAFPPGYRDQYDALEALADIDIIETLTEGALPRVR-AFRRFEDGPRTFR 551
            G V  L ++YG A P GY +  D L A A  D+ +         VR +F   E  P   R
Sbjct: 504  GVV--LANRYGKALPAGYVE--DVLPAAAAEDVRQLALLRGDDAVRMSFYHPEQRPEELR 559

Query: 552  FKLYLRGAAAPLAEVLPILERMGLKALIEDGFRLSIHEKDGPHSVWVHEFVLDDPAGEHI 611
            FK+Y  GA   L+EVLP LE +GL+ L E  + +    K G   +++ +F +        
Sbjct: 560  FKVYRSGADIALSEVLPQLENLGLRVLTEHVYDV----KTGGTPLFIQDFEVQPVGNLTF 615

Query: 612  VFDEVRQVFEEAFIAIWTGATENDGFNRIVLEMAVGWREAALLRALARYRQQSGLDPSQQ 671
              ++V  +FE+AF  IW    ENDGFNR+VL   + WR+ A+LR   +Y  Q+G+  SQ 
Sbjct: 616  SVEQVGSLFEDAFEQIWRVNAENDGFNRLVLGAKLSWRQVAMLRGYCKYLLQTGVAFSQN 675

Query: 672  VQEAALRDHPMVARLILDLFRVKFDP---------------AIRADLRT----------- 705
              E A   +P +A L+++LF  KFDP               A+  +++            
Sbjct: 676  YMEDAFNRYPAIAGLLVELFLAKFDPRREELGAVELKNARAALAGEMQALIPESVRQAHP 735

Query: 706  -------------RREQAEAVQFSIVEALQAVESLDADRVLRRLAALVGAIQRTNFYQLG 752
                         R EQ +A++ +I   L+ V SLD DR+LR   AL+    RT+F+Q  
Sbjct: 736  ALIDGLVAALEQPRAEQIKAIEEAIGVLLENVSSLDDDRILRSFVALIRGTLRTSFFQQW 795

Query: 753  ADGEPKSYISFKIASRELEDLPAPKPYREIYVSAPHVEGVHLRFGPVARGGLRWSDRRDD 812
             +G  + YISFK  S  + DLP P PYREI+VSAP VEG+HLRFG VARGGLRWSDRR+D
Sbjct: 796  -EGAYRGYISFKFDSHRVPDLPKPVPYREIFVSAPRVEGIHLRFGAVARGGLRWSDRRED 854

Query: 813  FRTEVLGLVKAQQVKNAVIVPVGSKGGFYPKQLPRGGDRDAIQAEAIRAYKTFLSGLLDL 872
            FRTEVLGLVKAQ VKN VIVPVGSKGGF  K+ P GGDRDA  AE I  Y+ F++GLLD+
Sbjct: 855  FRTEVLGLVKAQMVKNTVIVPVGSKGGFVVKRPPLGGDRDAQLAEGIACYRMFINGLLDI 914

Query: 873  TDNIDSDNQVVPPPSVIAHDAQDPYLVVAADKGTATFSDIANGVAESYGFWLGDAFASGG 932
            TDN+  + +VVPP  V+ HDA DPYLVVAADKGTATFSDIAN ++  +GFWLGDAFASGG
Sbjct: 915  TDNL-VEGKVVPPHDVVRHDADDPYLVVAADKGTATFSDIANAISLEHGFWLGDAFASGG 973

Query: 933  SVGYDHKVMGITARGAWEAVKRHFRELGKDIQTEAFTVVGVGDMSGDVFGNGMLLSKQTK 992
            S GYDHK MGITA+GAWE+VKRHFR LG+D QT+ FT VG+GDMSGDVFGNGMLLS+  +
Sbjct: 974  SNGYDHKGMGITAKGAWESVKRHFRALGRDSQTQDFTCVGIGDMSGDVFGNGMLLSRHIR 1033

Query: 993  LLAAFDHRHIFLDPNPDPAVSWAERDRMFKLPRSSWEDYDKSKISAGGGVFARSLKSIPL 1052
            LLAAFDHRHIFLDPNPD   S+ ER+RMFKLPRSSW+DYDKS ISAGGGV+ R+LK+IP+
Sbjct: 1034 LLAAFDHRHIFLDPNPDAERSFVERERMFKLPRSSWDDYDKSLISAGGGVYPRTLKAIPV 1093

Query: 1053 SAEVRAMLEIKAEA--VSPAELMTAILKSKAELLYLGGIGTYVKAKGETNADAGDKANDA 1110
            S EVRA L IK +A  ++P EL+ AILK+  +LL+ GGIGTYVKA  E++ADAGD+AN+A
Sbjct: 1094 SPEVRAALGIKGDATQMAPNELLNAILKAPVDLLWNGGIGTYVKAASESHADAGDRANNA 1153

Query: 1111 IRINGSDLRVKVVGEGANLGLTQAGRIEFAQAGGHINTDAIDNSAGVDSSDHEVNIKILT 1170
            +R NG++LR K+VGEG NLG TQ GRIE AQ G  +NTD IDNSAGVD+SDHEVNIKIL 
Sbjct: 1154 LRANGAELRCKMVGEGGNLGFTQKGRIEAAQHGVLLNTDFIDNSAGVDTSDHEVNIKILL 1213

Query: 1171 GILERGGQLDRESRNTLLASMTDDVAHHVLEHNYDQTLALTLLESDAVSEVDAQIRYMVN 1230
                + G+LD ++RN  LA+MTD+V   VL  NY Q  A+TL+E  +V  + +   ++  
Sbjct: 1214 DDAVQRGELDTDARNRQLAAMTDEVGQLVLWDNYRQNQAITLMERQSVRRLGSMAHFIRI 1273

Query: 1231 LEQRGRLDRRVEGLPTNTTLLERKAAGRGLTRPELAVLLAYGKLDLFDEIVASQSPDDPW 1290
            LE  G LDR+VE LP+ T L ERK  G+G+TRPEL+VLL+Y K+ L+ +++ S  P+DP+
Sbjct: 1274 LEGEGLLDRQVENLPSETELTERKTRGQGMTRPELSVLLSYDKIKLYQQLLDSDVPEDPY 1333

Query: 1291 FERTLRGYFPRAL-DQYADAMQKHRLKREIIATVVGNQMVNMCGPTFVSRLKAAAGADVN 1349
              + L  YFP  L ++YA+ MQ+HRLKREIIAT V N  +N  G TF+ R++   G    
Sbjct: 1334 LSKELVRYFPEPLHEKYAEHMQRHRLKREIIATAVTNSTINRMGATFMMRMQEDTGHGPA 1393

Query: 1350 AVVVGFTAAREILGIDGLWDQVNGLDNKASAEGQTALYKALAYALRSLTFWLARRAQRDA 1409
            A+   +TAAREILG   LW ++  LD+K + E Q      +   LR LT WL  R     
Sbjct: 1394 AIAKAYTAAREILGARELWAEIEALDSKVAEETQLDAIMQIWSLLRHLTRWLLSR-PGGT 1452

Query: 1410 ANVQTLVEAYGPSVAALKALAPAILSPFEQKAVSKRVKAYVADGAPEALALSVAALQPLT 1469
              +   V+ Y   VAAL    P  L+P  +   S   + +   G P  L++ +A +  L 
Sbjct: 1453 LEIAANVDRYQAGVAALYEAVPDTLTPTGKADFSTSQEKWEGLGLPTELSVRMARIPELR 1512

Query: 1470 TAADLVDLANASSWSVENVARLYHQVGAAFGFDRLRGAAGSFVGGDAFERLAVRRLIEDM 1529
               D++++A  S   V+ VA +++++G A   + LR    +      +   A   L++++
Sbjct: 1513 AMLDMLEVAQQSGQPVDQVAGVFYELGEALDLEWLRSQIEALPVEGHWHAQARGSLLDEL 1572

Query: 1530 LTEQTSITQQVLKFAANAQ 1548
              +  ++  QVL  A  ++
Sbjct: 1573 NHQHRALALQVLALAGGSK 1591


Lambda     K      H
   0.319    0.135    0.390 

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: 5631
Number of extensions: 239
Number of successful extensions: 12
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: 1607
Length of database: 1644
Length adjustment: 52
Effective length of query: 1555
Effective length of database: 1592
Effective search space:  2475560
Effective search space used:  2475560
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: 61 (28.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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
the source code
instructions for running GapMind on your computer

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 catabolism of small carbon sources