Alignments for a candidate for gdhA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Burkholderia phytofirmans PsJN

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate BPHYT_RS22475 BPHYT_RS22475 NAD-glutamate dehydrogenase

Query= uniprot:G8AE86
         (1618 letters)



>FitnessBrowser__BFirm:BPHYT_RS22475
          Length = 1613

 Score = 1568 bits (4061), Expect = 0.0
 Identities = 850/1625 (52%), Positives = 1067/1625 (65%), Gaps = 25/1625 (1%)

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

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

Query: 121  TVHLVIHPVVRVKRDADGQLAELYEPAAAPTDAAPE--SFMHVEVGAVTGAAALDQAREG 178
             +H V+HPV R+ R  DG +A + + A   TD+     SF+H EV     AA LD  R+ 
Sbjct: 120  ALHSVVHPVFRIWRAPDGSIARVSQGAEEATDSRSHLTSFIHFEVDRCGDAAKLDALRDE 179

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

Query: 239  TFLGYREYRFESGADGADSSLGLVAGSGLGILRDDSVTVFDGLRNYATLPPDVRDFLRNP 298
            TFLG R+Y       G    L  V GSGLGILRD       G      LPP   + +   
Sbjct: 233  TFLGQRDYELVQHDIGY--GLRAVPGSGLGILRDALRPA--GAAEITPLPPAAAEIISGS 288

Query: 299  RVLMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPREIPYLR 358
              + +TK N  + VHR   +D   IK   A+G++ GER   GL+TS AY  S  EIP +R
Sbjct: 289  SPIFLTKANSRATVHRPGYLDYVGIKLTGADGKVTGERRFIGLYTSTAYFVSAAEIPIVR 348

Query: 359  RKVAEVMELAGFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQERQRLAL 418
            RK A ++  AGF P+GH  K+L+ +LETYPRDELFQ +  +L DIA+G+L LQE QR  L
Sbjct: 349  RKCANIVRRAGFLPKGHLAKSLVTVLETYPRDELFQAEENQLYDIALGVLRLQEHQRTRL 408

Query: 419  FVRKDPFERFASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVLARLHFI 478
            F+R+D F+RF SCLV+VPRD+Y+T LR+RI ++L  A++G    FT  L+ES LAR+HF+
Sbjct: 409  FIRRDRFDRFVSCLVFVPRDKYNTDLRQRIANLLVDAFNGESVEFTPLLSESTLARIHFV 468

Query: 479  IRTEPGRVPTVDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADAFPTAYR 538
            +  +PG +P VD  +LEARLVQ +R W D L DAL++A GEEQG  L + Y D+FP  YR
Sbjct: 469  VHAKPGGMPNVDTRELEARLVQVARRWQDDLADALLDAFGEEQGNRLLQHYGDSFPAGYR 528

Query: 539  EEFNAEAAVFDIERIEKATAQGTLGINLYRPLEAEGDELHVKIYHEGRPVPLSDVLPMLE 598
            +++ A  AV DIE IE       L +NLYRP+E+       K+Y  G P+ LS  LPMLE
Sbjct: 529  DDYPARTAVRDIELIEHVQGSERLAMNLYRPIESGPRAFRFKVYRAGLPIALSRSLPMLE 588

Query: 599  HMDLKVITEAPFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQDAFAAVWDGRME 658
            H+ ++V  E P+ I   G A P WIHDF     +    D   VK+ F++AF  VW G +E
Sbjct: 589  HLGVRVDEERPYLIEALG-ATPAWIHDFGLELADDAEFDIERVKDLFEEAFEKVWTGAIE 647

Query: 659  DDGFNRLVLRAGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPAIARKLVALFHS 718
             D FNRLVLRA L AREVT+LRAYAKYLRQ    +    +E  + G+PAIAR LV LF +
Sbjct: 648  SDDFNRLVLRAQLNAREVTILRAYAKYLRQVGSTFSDAYIERAVTGNPAIARMLVELFIA 707

Query: 719  RFDPA---RRSQNDPGLAAEIERALDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGR 775
            RF+P     R     G    I+ ALD V NLDEDRILR+FL ++  T RTN Y+  ADG 
Sbjct: 708  RFNPVLGETREARVDGWLHTIDSALDQVPNLDEDRILRQFLGVIKATKRTNYYRFDADGH 767

Query: 776  PKTYLSFKIDSRNIDDLPLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTE 835
            PK YLSFK D   +  LP P+PM E++VYSPR+EGVHLRGG+VARGG+RWSDRREDFRTE
Sbjct: 768  PKPYLSFKFDPAQVPGLPEPKPMFEIWVYSPRVEGVHLRGGRVARGGLRWSDRREDFRTE 827

Query: 836  ILGLMKAQMVKNTVIVPVGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDITDN 895
            +LGLMKAQMVKN VIVPVGSKGGFVVK PPP +  R+A + EGI CY+T +RGLLD+TDN
Sbjct: 828  VLGLMKAQMVKNVVIVPVGSKGGFVVKNPPPQTE-RDAWMREGIACYQTFLRGLLDVTDN 886

Query: 896  LDAQGAVVPPPEVVRHDGDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGGSAG 955
            L A   +VPPP+VVRHD DDPYLVVAADKGTATFSD AN++S ++GFWL DAFASGGS G
Sbjct: 887  L-AGTTIVPPPDVVRHDPDDPYLVVAADKGTATFSDYANAISQEYGFWLDDAFASGGSVG 945

Query: 956  YDHKKMGITARGAWESVKRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLA 1015
            YDHKKM ITARGAWESVKRHFRE+G DTQT DFTVVGVGDMSGDVFGNGMLLS HI+L+A
Sbjct: 946  YDHKKMAITARGAWESVKRHFREMGVDTQTMDFTVVGVGDMSGDVFGNGMLLSPHIKLVA 1005

Query: 1016 AFDHRHIFIDPDPDAARSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLELTPE 1075
            AFDHRHIF+DP+PD A S  ER RLF L RSSWADYD SL+SAGG VF RSAK++ L+P 
Sbjct: 1006 AFDHRHIFLDPNPDPAVSLAERGRLFILDRSSWADYDPSLISAGGGVFPRSAKTIPLSPA 1065

Query: 1076 IRQRFGIAKDHVTPLELMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALRIDG 1135
            ++   GI+   + P ELM+ +L+A VDLL+ GGIGTY+KA+ E++ +VGD+ANDA+R++G
Sbjct: 1066 VQSVLGISAPALAPAELMRAILQAPVDLLYNGGIGTYVKASRESHLQVGDRANDAIRVNG 1125

Query: 1136 RDVRAKVIGEGANLGVTQRGRIEAAQHGVRLNTDAIDNSAGVDTSDHEVNIKILLNDVVV 1195
             D++ KV+ EG NLG+TQ GRIE AQ G R+NTDAIDNSAGVD SDHEVNIKILL  VV 
Sbjct: 1126 SDLQCKVVAEGGNLGLTQLGRIEFAQRGGRINTDAIDNSAGVDCSDHEVNIKILLGLVVS 1185

Query: 1196 RGDMTLKQRDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLEKAG 1255
             G+MT KQR+ LLA MTDEV  LVL DNY Q+QAL++A   G + L+A+ARL+R LE+AG
Sbjct: 1186 DGEMTEKQRNALLAEMTDEVGLLVLQDNYYQTQALSIAGRYGVELLDAEARLMRYLERAG 1245

Query: 1256 RLNRAIEYLPDEEELSARMANREGLTRPELAVLLAYAKITLYDDLLASDLPDDPFMADDL 1315
            RLNR IE+LP +EE++ R A ++GLT PE AVLLAY+K+ LYD LL S +P+DP ++D L
Sbjct: 1246 RLNRVIEFLPTDEEVAERQAAKQGLTTPERAVLLAYSKMWLYDALLESPMPEDPLVSDML 1305

Query: 1316 TRYFPKPLRKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARA 1375
              YFPKPLR+  +E + RH LRREI+AT +TN+LVNR G  FV  +ME+T   P ++ RA
Sbjct: 1306 VEYFPKPLRQRFSEPMQRHPLRREILATHLTNALVNRVGCEFVHRLMEETDAQPGEIVRA 1365

Query: 1376 YTIVRDAFGLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQ----QPLD 1431
              + RD F L  +W  I+ LD  V   +Q  M +E  R +ER+A WFL   Q       D
Sbjct: 1366 IIMARDVFDLDDVWRSIDALDNRVADDIQARMFVEVARLVERSALWFLRQLQSGAVSDRD 1425

Query: 1432 IARETEAFRPGIETLLAGLDNVLDAEETARLTARVASYQEQGVPAELARRMAALPVLAAA 1491
            +A      R   + L      +L   +   L+ R   + + GV +ELA R+A   + AA 
Sbjct: 1426 VAGLLARCRDAAQRLAPQWPALLPGADLEALSERQRVFADAGVDSELAVRIAGGEISAAL 1485

Query: 1492 PDLVRIAGRTGRGVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQAVAALVDDLFA 1551
             D+  +A  +GR +  VA VYF LG      W+ ++AAA     HW   A A  V D+  
Sbjct: 1486 LDIAEVASTSGRSLELVAGVYFALGTLLNSSWISERAAALPVPTHWDMLARATAVADIAR 1545

Query: 1552 HQTALTTRVL-EAVDQLPAEAPVEAWIAHRRPVVERVEQLLSELRTQPNVDLSMLAVANR 1610
             + ALTT  L +A D    EA VEAW   R   +ER   LL++LR      LSML V  R
Sbjct: 1546 LKRALTTSALADADDASTPEALVEAWREKRTVQLERYAHLLADLRATGGASLSMLLVIVR 1605

Query: 1611 QLRGL 1615
            ++  L
Sbjct: 1606 EMAAL 1610


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: 5951
Number of extensions: 283
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: 1613
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1562
Effective search space:  2447654
Effective search space used:  2447654
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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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