GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Paraburkholderia bryophila 376MFSha3.1

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate H281DRAFT_03183 H281DRAFT_03183 glutamate dehydrogenase (NAD)

Query= uniprot:G8AE86
         (1618 letters)



>FitnessBrowser__Burk376:H281DRAFT_03183
          Length = 1617

 Score = 1577 bits (4083), Expect = 0.0
 Identities = 855/1628 (52%), Positives = 1083/1628 (66%), Gaps = 27/1628 (1%)

Query: 1    MALRAEQLKDELTEEVVRQVRERLGRSRAAPAERFVRQFYDNVPPDDIIQAPAEQLYGAA 60
            M  + E+    L  +VV   R RL        E F+R +YD V  DD+       LYGAA
Sbjct: 1    MQAKNEEAVTHLLNDVVEFARARLPEPTFHIVEPFLRHYYDFVDVDDLQSRSIPDLYGAA 60

Query: 61   LAMWQWGQQREATDRAKVRVYNPRVEEHGWQSHRTVVEIVNDDMPFLVDSVTAELNRQGL 120
            LA WQ  Q R    R ++RVYNP +E+HGW S  TV+EIVNDDMPFLVDSV+  +NRQGL
Sbjct: 61   LAHWQTAQ-RFVPGRERLRVYNPILEQHGWHSDHTVIEIVNDDMPFLVDSVSMAVNRQGL 119

Query: 121  TVHLVIHPVVRVKRDADGQLAELYEPA--AAPTDAAPESFMHVEVGAVTGAAALDQAREG 178
             +H V+HPV R+ R  DG +A + + +  AA T +   SF+H EV     AA LD  R+ 
Sbjct: 120  ALHSVVHPVFRIWRGPDGDIARVTQGSEEAADTRSQLASFIHFEVDRCGDAAKLDALRDD 179

Query: 179  LERVLADVRAAVADWRAMRQQVRAAIVEADCARAAVPAIIPDDEVDEAKAFLSWADDDHF 238
            + +VL DVRAAV DW  + +  R  I       +   A+       EA+AFL W   DHF
Sbjct: 180  IAKVLRDVRAAVEDWPKIVELARVTIKAMKVGESGPDAM-------EARAFLEWMVADHF 232

Query: 239  TFLGYREYRFESGADGADSSLGLVAGSGLGILRDDSVTVFDGLR---NYATLPPDVRDFL 295
            TFLG+R+Y  E    G    L  V GSGLGI+RD+ +   DG         LPP   + +
Sbjct: 233  TFLGHRDY--ELVQQGTGYGLRAVPGSGLGIMRDE-LRATDGAAASPEVTVLPPAAAEII 289

Query: 296  RNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPREIP 355
             +   + +TK N  + VHR   +D   IK   A+G+++GER   GL+TS AY  S  EIP
Sbjct: 290  SSASPIFLTKANSRATVHRPGYLDYVGIKLAGADGKVVGERRFIGLYTSTAYFVSAAEIP 349

Query: 356  YLRRKVAEVMELAGFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQERQR 415
             +RRK A ++  AGF P+GH  K+L+ +LETYPRDELFQ    +L DIA+G+L LQE QR
Sbjct: 350  IVRRKCANIVRRAGFLPKGHLAKSLVTVLETYPRDELFQADENQLYDIALGVLRLQEHQR 409

Query: 416  LALFVRKDPFERFASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVLARL 475
              LFVR+D F+RF SCLV+VPRD+Y+T LR+RI ++L  A++G    FT  L+ES LAR+
Sbjct: 410  TRLFVRRDRFDRFVSCLVFVPRDKYNTDLRQRIANLLTEAFNGASVEFTPLLSESTLARI 469

Query: 476  HFIIRTEPGRVPTVDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADAFPT 535
            HF++  +PG +P VD  +LEARLVQ SR W D L DAL++A GEEQG  L + YAD+FP 
Sbjct: 470  HFVVHAKPGGMPDVDTRELEARLVQVSRRWQDDLADALLDAFGEEQGNRLLQHYADSFPP 529

Query: 536  AYREEFNAEAAVFDIERIEKATAQGTLGINLYRPLEAEGDELHVKIYHEGRPVPLSDVLP 595
             YR+++ A  AV DIE IE+      L +NLYRP+EA       K+Y  G P+ LS  LP
Sbjct: 530  GYRDDYAARTAVRDIELIERVQGSERLAMNLYRPIEAGPRAFRFKVYRAGMPIALSRSLP 589

Query: 596  MLEHMDLKVITEAPFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQDAFAAVWDG 655
            MLEH+ ++V  E P+ I   G A P WIHDF     +    D   VK+ F+DAF  VW G
Sbjct: 590  MLEHLGVRVDEERPYLIEALG-ATPAWIHDFGLEVVDDAEFDIERVKDLFEDAFEQVWTG 648

Query: 656  RMEDDGFNRLVLRAGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPAIARKLVAL 715
             +E D FNRLVLRA L+AREVT+LRAYAKYLRQ    +    +E  + G+PAIAR LV L
Sbjct: 649  AIESDDFNRLVLRAQLSAREVTILRAYAKYLRQVGSTFSDAYIERAVTGNPAIARMLVEL 708

Query: 716  FHSRFDPA---RRSQNDPGLAAEIERALDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGA 772
            F +RFDP+    R      L   I+ ALD V NLDEDRILR+FL ++  T RTN Y   A
Sbjct: 709  FIARFDPSLAGTRETRVENLLKTIDSALDQVPNLDEDRILRQFLGVIKATQRTNYYVFDA 768

Query: 773  DGRPKTYLSFKIDSRNIDDLPLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDF 832
            DG+PK YLSFK +   +  LP P+PM E++VYSPR+EGVHLRGG+VARGG+RWSDRREDF
Sbjct: 769  DGQPKPYLSFKFNPAQVPGLPEPKPMFEIWVYSPRVEGVHLRGGRVARGGLRWSDRREDF 828

Query: 833  RTEILGLMKAQMVKNTVIVPVGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDI 892
            RTE+LGLMKAQMVKN VIVPVGSKGGFVVK PPP S  R+A + EGI CY+T +RGLLD+
Sbjct: 829  RTEVLGLMKAQMVKNVVIVPVGSKGGFVVKNPPPQSE-RDAWMREGIACYQTFLRGLLDL 887

Query: 893  TDNLDAQGAVVPPPEVVRHDGDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGG 952
            TDNL A   VVPP +VVRHD DDPYLVVAADKGTATFSD AN++S ++GFWL DAFASGG
Sbjct: 888  TDNL-AGTTVVPPRDVVRHDPDDPYLVVAADKGTATFSDYANAISQEYGFWLDDAFASGG 946

Query: 953  SAGYDHKKMGITARGAWESVKRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIR 1012
            S GYDHKKM ITARGAWESVKRHFRE+G DTQT DFTVVG+GDMSGDVFGNGMLLS HIR
Sbjct: 947  SVGYDHKKMAITARGAWESVKRHFREMGVDTQTMDFTVVGIGDMSGDVFGNGMLLSPHIR 1006

Query: 1013 LLAAFDHRHIFIDPDPDAARSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLEL 1072
            L+AAFDHRHIF+DP+PD A S  ER RLF L RSSWADYD SL+SAGG VF R+AK++ L
Sbjct: 1007 LVAAFDHRHIFLDPNPDPAASIAERGRLFLLDRSSWADYDPSLISAGGGVFPRTAKTIAL 1066

Query: 1073 TPEIRQRFGIAKDHVTPLELMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALR 1132
            +P ++   GI+   ++P ELM+ +L+A VDLL+ GGIGTY+KA+ ET+ +VGD+ANDA+R
Sbjct: 1067 SPAVQSVLGISAAALSPAELMRAILQAPVDLLYNGGIGTYVKASRETHLQVGDRANDAIR 1126

Query: 1133 IDGRDVRAKVIGEGANLGVTQRGRIEAAQHGVRLNTDAIDNSAGVDTSDHEVNIKILLND 1192
            ++G D+R KV+ EG NLG+TQ GRIE AQ G R+NTDAIDNSAGVD SDHEVNIKILL  
Sbjct: 1127 VNGADLRCKVVAEGGNLGLTQLGRIEFAQRGGRINTDAIDNSAGVDCSDHEVNIKILLGL 1186

Query: 1193 VVVRGDMTLKQRDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLE 1252
            VV  G+MT KQR+ LLA MTDEV  LVL DNY Q+QAL++A   G + L+A+ RL+R LE
Sbjct: 1187 VVADGEMTAKQRNALLAEMTDEVGLLVLTDNYYQTQALSIAGRYGVELLDAETRLMRYLE 1246

Query: 1253 KAGRLNRAIEYLPDEEELSARMANREGLTRPELAVLLAYAKITLYDDLLASDLPDDPFMA 1312
            +AGRLNRAIE+LP++EE++ R A ++GLT PE AVLLAY+K+ LYD LL S +P+DP ++
Sbjct: 1247 RAGRLNRAIEFLPNDEEVAERQAAKQGLTTPERAVLLAYSKMWLYDALLDSSVPEDPLVS 1306

Query: 1313 DDLTRYFPKPLRKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADV 1372
            D L  YFP+PLR+  +E + RH LRREI+AT +TN+LVNR G  FV  +ME+T   P D+
Sbjct: 1307 DMLIEYFPRPLRQRFSEPMQRHPLRREILATHLTNALVNRVGCEFVHRLMEETDAQPGDI 1366

Query: 1373 ARAYTIVRDAFGLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQQP--- 1429
             RA  + RD F L  +W  I+ LD  V   +Q  M +E  R +ER+A WFL     P   
Sbjct: 1367 VRACIMARDVFDLDDVWRSIDALDNRVADDVQARMFVEVARLVERSALWFLRHLSSPGVN 1426

Query: 1430 -LDIARETEAFRPGIETLLAGLDNVLDAEETARLTARVASYQEQGVPAELARRMAALPVL 1488
              D+       R   + L      +L A +   L+ R     + GV +ELA R+A+  + 
Sbjct: 1427 SDDVTGLLARCRDAAQRLAPQWPALLPAADLEALSERQRVLVDAGVDSELAVRIASGEIS 1486

Query: 1489 AAAPDLVRIAGRTGRGVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQAVAALVDD 1548
            AA  D+  +A    R +  VA VYF LG      W+ ++AAA  A++HW   A A+ + +
Sbjct: 1487 AALLDIAEVASTCKRKLELVAGVYFALGTLLNYNWISERAAALPAQSHWDMLARASALAE 1546

Query: 1549 LFAHQTALTTRVLEAVDQLPA-EAPVEAWIAHRRPVVERVEQLLSELRTQPNVDLSMLAV 1607
            L   + ALT   L + D     +A V+AW   R   +ER  +LL++LR      LSML V
Sbjct: 1547 LARLKRALTMSALASADDAATPDALVQAWRDKRATQLERYARLLADLRATGGASLSMLLV 1606

Query: 1608 ANRQLRGL 1615
              R++  L
Sbjct: 1607 IVREMAAL 1614


Lambda     K      H
   0.320    0.136    0.399 

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: 5922
Number of extensions: 272
Number of successful extensions: 13
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: 1618
Length of database: 1617
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1566
Effective search space:  2453922
Effective search space used:  2453922
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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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