Alignments for a candidate for gdhA in Rhizobium johnstonii 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Rhizobium johnstonii 3841

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate WP_011654049.1 RL_RS24285 NAD-glutamate dehydrogenase

Query= uniprot:G8AE86
         (1618 letters)



>NCBI__GCF_000009265.1:WP_011654049.1
          Length = 1592

 Score = 1176 bits (3043), Expect = 0.0
 Identities = 672/1527 (44%), Positives = 917/1527 (60%), Gaps = 47/1527 (3%)

Query: 95   TVVEIVNDDMPFLVDSVTAELNRQGLTVHLVIHPVVRVKRDADGQLAELYEPAAAPTDAA 154
            +V+ + + +MPFL +SV  E+      + + +HP++ +++   G+   LY  A  P+D A
Sbjct: 87   SVLSVTDQNMPFLFESVMGEVTSTYRDLFMAVHPILVMEK---GKAPALYS-ADHPSDPA 142

Query: 155  PE-SFMHVEVGAVTGAAALDQAREGLERVLADVRAAVADWRAMRQQVRAAIVEADCARAA 213
               S + + +  +    A D  +  +E+VL  VR +V+DW+ M  ++   I E     AA
Sbjct: 143  NRVSHIQLHIAPLNSTQAADLVKR-IEKVLEQVRLSVSDWKPMLSKIDGVIAEL----AA 197

Query: 214  VPAIIPDDEVDEAKAFLSWADDDHFTFLGYREYRFESGADGADSSLGLVAGSGLGILRDD 273
              A     + DEA AFL+W  D++FTFLG REY +     GA++ +    G+GLGIL + 
Sbjct: 198  NGASRKKADRDEAVAFLTWLRDENFTFLGMREYVYSG--KGAEAKVERDKGAGLGILSNP 255

Query: 274  SVTVFDGLRNYATLPPDVRDFLRNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRII 333
             V V    ++  T  P++  FL  P  L+VTK N  S VHR   MD   +KRFDA+G + 
Sbjct: 256  DVLVLRTGKDAVTTTPEILAFLDGPDFLIVTKANVKSIVHRRAYMDYVGVKRFDADGNVT 315

Query: 334  GERLVAGLFTSVAYNRSPREIPYLRRKVAEVMELAGFDPQGHDGKALLHILETYPRDELF 393
            GE  + GLFTS AY     EIP LR K+ +V E  GFDP  H G+ L + LE+YPRD+LF
Sbjct: 316  GELRIVGLFTSTAYTSLASEIPLLRSKIEKVKEHFGFDPMSHSGRMLDNTLESYPRDDLF 375

Query: 394  QIQVPELLDIAVGILHLQERQRLALFVRKDPFERFASCLVYVPRDRYDTTLRRRIQSILE 453
            QI    L   A  I  L +R R+ +  R D F+RF S +VYVPR+ YD+ +R RI + L+
Sbjct: 376  QIDTTLLASFAEQINDLGDRPRVRVLPRIDHFDRFVSVIVYVPREEYDSIVRERIGTYLK 435

Query: 454  AAYDGTCTGFTTQLTESVLARLHFIIRTEPGRVPTVDATDLEARLVQASRGWDDHLRDAL 513
              YDG  + +     E  +AR+HFII    G+ P +    LE  + + +  WDD   +AL
Sbjct: 436  TVYDGRVSAYYPAFPEGGVARVHFIIGRSGGKTPRIPQAKLEQVIREITARWDDRF-EAL 494

Query: 514  VEAHGEEQGRTLFRRYADAFPTAYREEFNAEAAVFDIERIEKATAQGTLGINLY-RPLEA 572
                  +           +   A+++ F  E  V D+  I        L I+ Y R  E 
Sbjct: 495  AGVKAPKI----------SVDQAFQDSFTPEETVADLADIGACATGEPLRIHFYHRQEEE 544

Query: 573  EGDELHVKIYHEGRPVPLSDVLPMLEHMDLKVITEAPFEIAIA---GHAAPVWIHDFTAR 629
            +G  L +KI+H G  + LS  +P+LE++   V++E  F+I +    G    V +HD    
Sbjct: 545  QGRILSLKIFHAGGQLALSRRVPLLENLGFNVVSERTFDIGVPVADGEKKLVVLHDMELE 604

Query: 630  SQNGLPIDCAMVKEKFQDAFAAVWDGRMEDDGFNRLVLRAGLTAREVTVLRAYAKYLRQA 689
            ++NG  ID        ++ F A + G +++D FNRL+L AGL+ARE  VLRAYA+YLRQA
Sbjct: 605  ARNGGEIDLQRYGAALEEGFVAAFAGTIDNDSFNRLILSAGLSARETNVLRAYARYLRQA 664

Query: 690  RIPYGQDVVESTLAGHPAIARKLVALFHSRFDPARRSQNDPGLAAEIERALD----GVKN 745
             IPY QD + +TL  +P +A  +  LFH   D     +      AE+ +A++     V +
Sbjct: 665  GIPYSQDYIATTLDKYPGVAAAIFRLFHDTLDTRLTEKARVKKLAELHQAIETELANVPS 724

Query: 746  LDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYLSFKIDSRNIDDLPLPRPMVEVFVYS 805
            LD+DRILRR++N++  TLRTN +Q   DG PK  L+FK+D   +D LP P+P  E+FVY 
Sbjct: 725  LDDDRILRRYVNIVDATLRTNYFQKNPDGSPKPMLAFKLDPHLVDGLPEPKPFREMFVYG 784

Query: 806  PRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKNTVIVPVGSKGGFVVKRPP 865
              +EGVHLR GKVARGG+RWSDR ED+RTE+LGL+KAQ VKN VIVPVG+KGGF  K+ P
Sbjct: 785  VEVEGVHLRFGKVARGGLRWSDRAEDYRTEVLGLVKAQQVKNAVIVPVGAKGGFYPKKLP 844

Query: 866  PPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQGAVVPPPEVVRHDGDDPYLVVAADKG 925
              S  R+     G E YKT +R LL ITDN+     +VPP + VR DGDDPY VVAADKG
Sbjct: 845  V-SGSRDETFNAGREAYKTYIRTLLSITDNISGAD-IVPPKDTVRLDGDDPYFVVAADKG 902

Query: 926  TATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKKMGITARGAWESVKRHFRELGHDTQT 985
            TATFSD AN+++ + GFWL DAFASGGSAGYDHKKMGITARGAWE+VKRHFRE+  D QT
Sbjct: 903  TATFSDTANALAQEAGFWLDDAFASGGSAGYDHKKMGITARGAWETVKRHFREMDIDIQT 962

Query: 986  QDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHRHIFIDPDPDAARSWEERQRLFDLPR 1045
              FTV GVGDMSGDVFGNGMLLS  IRL+AAFDHR I IDPDPD  ++  ERQRLFDLPR
Sbjct: 963  TPFTVAGVGDMSGDVFGNGMLLSPKIRLIAAFDHRDIVIDPDPDMEKTLTERQRLFDLPR 1022

Query: 1046 SSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRFGIAKDHVTPLELMQTLLKAEVDLLW 1105
            SSW D+D S+LS G  +  RSAKS+ LTPE     GI K   TP E+M  +LK+ VDLLW
Sbjct: 1023 SSWQDFDKSVLSKGAMIISRSAKSVTLTPEAVAAIGIDKAVATPFEIMTAILKSPVDLLW 1082

Query: 1106 FGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRAKVIGEGANLGVTQRGRIEAAQHGVR 1165
            FGGIGTY+KA+ ET+ EVGD+AND +RI   +VRAKVIGEGANLGVTQ+GRI     G R
Sbjct: 1083 FGGIGTYVKASSETDTEVGDRANDPIRITAAEVRAKVIGEGANLGVTQKGRIAYGLKGGR 1142

Query: 1166 LNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMTLKQRDQLLAAMTDEVAGLVLADNYL 1225
             N+DAIDNSAGV+TSD EVNIKI L   +  G +T  +RDQLL++MT EVA LVL +NYL
Sbjct: 1143 CNSDAIDNSAGVNTSDVEVNIKIALAAAMHDGRLTRVKRDQLLSSMTSEVATLVLRNNYL 1202

Query: 1226 QSQALTVARAQGPDALEAQARLIRSLEKAGRLNRAIEYLPDEEELSARMANREGLTRPEL 1285
            QS A+++   +G        R +  LE AG+LNR +E LPD++ L+ R A  + LTRPE+
Sbjct: 1203 QSLAISLTERKGTANGLELGRFMSVLEGAGQLNRKVETLPDDQTLAERYAAGKPLTRPEI 1262

Query: 1286 AVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFPKPLRKAHAEAVGRHRLRREIIATSV 1345
             VL++YAKI L+D L ASDLPDDP+    L  YFP  ++K++A  +  HRL+REI+AT +
Sbjct: 1263 GVLVSYAKIVLFDALAASDLPDDPYFIATLLNYFPVKMQKSNAGDIASHRLKREIVATVL 1322

Query: 1346 TNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVRDAFGLRSLWTGIEDLDTVVPAALQT 1405
             N  +NR GP+F   MM+ T     +V RA  + RD F L  LW   + LD  +   LQ 
Sbjct: 1323 ANEAINRGGPSFTVAMMDATAASAPEVVRAAIVARDGFDLTRLWAETDALDGKISGDLQ- 1381

Query: 1406 SMILETVRH----MERAAAWFLASCQQPLDIARETEAFRPGIETLLAGLDNVLDAEETAR 1461
            + I E + H    + R       +    +++    +A    ++T  AG       +    
Sbjct: 1382 NRIYEEISHSFIVLTRLLLKTGMTKADMVEVISRLQAALKKLKTAFAG-------QVAGE 1434

Query: 1462 LTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGRTGRGVADVAAVYFMLGRRFGL 1521
            +  R A Y + G+P +LA  +A+LP+ A  P++++IA RTG  +   A  Y  + + F +
Sbjct: 1435 VAVRQAEYSQAGLPEKLAADIASLPIFALVPEIMQIAERTGEPLVRAAENYIAVSQTFRI 1494

Query: 1522 EWLRDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRVLEAVDQLPAEAPVEAWIAHRR 1581
              L          +H++  A+A  +D + + +  +    L   D    + PV+AW A  R
Sbjct: 1495 GRLLAAGGRILTSDHYENLALARSIDQIASARRDIVISALS--DHGKEKLPVQAWHAQDR 1552

Query: 1582 PVVERVEQLLSELRTQPNVDLSMLAVA 1608
              + R+ + LS L    + +L+ + VA
Sbjct: 1553 IRINRILEELSSLSDGGDPNLARITVA 1579


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: 5487
Number of extensions: 253
Number of successful extensions: 14
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1618
Length of database: 1592
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1541
Effective search space:  2414747
Effective search space used:  2414747
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 Apr 09 2024. 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 2024 update 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