Alignments for a candidate for gdhA in Kocuria turfanensis HO-9042

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Kocuria turfanensis HO-9042

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_084271636.1 AYX06_RS13840 NAD-glutamate dehydrogenase

Query= BRENDA::Q8CJY0
         (1653 letters)



>NCBI__GCF_001580365.1:WP_084271636.1
          Length = 1641

 Score = 1266 bits (3276), Expect = 0.0
 Identities = 744/1657 (44%), Positives = 992/1657 (59%), Gaps = 97/1657 (5%)

Query: 49   PDYASVFAFLQRYYRHTAPEDLADRDPVDIFGAAVSHYRLAENRPQGTANVRVHTPTVEE 108
            P +    A++  YYRH   EDL  R    +   A  H+ +   R  G   V V       
Sbjct: 24   PQWDGDRAWINEYYRHVPQEDLLARTEEQLRERADHHHEVGRVRAPGEIAVGVRQED--- 80

Query: 109  NGWTCSHSVVEVVTDDMPFLVDSVTNELTRQGRGIHVVVHPQIVVRRDIAGKLVEVLAGP 168
                 S+SVV VVT+D+P+LV +V  E+  +  G  +V+HP +V  RD     +  L   
Sbjct: 81   -----SNSVVFVVTEDVPYLVSTVNAEIAAKWGGARLVIHPVLVATRDEGSHELRELQQV 135

Query: 169  P---------AADLPHDAH----------VESWIHVEIDRETDRGDLKQITADLLRVLND 209
            P            LP  A+          VESWI VE+ R       +Q+   L  +L D
Sbjct: 136  PDFSASASGDTTALPSLANFRASGGTRHVVESWISVELSRTISDETAQQLVDRLSTLLRD 195

Query: 210  VRETVEDWGKMRDAAVRIA---DQLSTEATPEDLPARELEEARELLRWLADDHFTFLGYR 266
            V+   ED  +++    R++   D+L T   P       +  +++ LRWL   +F  +G++
Sbjct: 196  VQRVDEDQEQLKARVERLSGELDRLRTLELPGGGHPPMVGPSQDFLRWLIGGNFILMGFK 255

Query: 267  EYQLRED-DSLAAVA--GTGLGILRSDPHHAADESHPVSPSFERLPADARAKAREHRLLV 323
            EY L E  D LA V+  GTGLG+L           H   P  ++L    R  ARE   L 
Sbjct: 256  EYDLEETGDGLALVSRPGTGLGLL---------VEHEGKPHRQQLTGLGREHAREAGTLF 306

Query: 324  LTKANSRATVHRPSYLDYVGVKKFDENGNVVGERRFLGLFSSAAYTESVRRVPVVRRKVE 383
            +TKAN R+++HR  YLDYVGV K+D+ G +VGE   LGLF+  AY    R  P+++ K+ 
Sbjct: 307  VTKANRRSSIHRREYLDYVGVAKYDDEGRIVGEYLVLGLFTRRAYNTPARETPLLKEKLA 366

Query: 384  EVLERAGFSPNSHDGRDLLQILETYPRDEMFQTSVEELEPIVTSVLYLQERRRLRLYLRQ 443
            EV +R GF  +SH  RDL+  +E YPRDE+F  + +EL  I+  V+ L ERR+ RL+LRQ
Sbjct: 367  EVADRFGFLEDSHSARDLMGNIEDYPRDELFHMTADELYDIMRGVMGLDERRQTRLFLRQ 426

Query: 444  DEYGRYYSALVYLPRDRYTTGVRLRIIDILKEELGGTSVDFTAWNTESILSRLHFVVRVP 503
            D +GR+ SA+V+LPRDRY T VR RI   L+      S+DF A  + S L+RL F +R+P
Sbjct: 427  DHFGRFMSAVVFLPRDRYNTSVRGRIEAELRRTFDAESIDFDARLSASTLARLFFRIRLP 486

Query: 504  QGTELPHLSDADKERVEARLVEAARSWADGFGEALTAEFGEERAAELLRLYGSAFPEGYK 563
               ++      D+  +EARL  A RSW++    A+  EF E+ A      +  AFP+ Y+
Sbjct: 487  YTGQVQSF---DRAGLEARLRAAVRSWSEALVRAIHREFPEDLARRHAENWAEAFPDAYR 543

Query: 564  ADHGPRSAVADLGHLEQL---DEETTFALSLYEPVGAAPEERRFKIYQKGGSVSLSAVLP 620
            AD+  + AV DL   E+L   D +    + + +  G      R  IY    S+SL+ +LP
Sbjct: 544  ADYEIQEAVEDLQRCEELWGRDPDLPAEVRVVDDPGGV----RLNIYLTR-SLSLTELLP 598

Query: 621  VLSRLGVEVTDERPYELRCADRTTAWIYDFGLRMPKAPSGGADYLG-DDAR--ERVQDAF 677
            +L  LG+ V D++PYE+  AD     +YDFG+R+P+    G D +G +DAR  + ++D  
Sbjct: 599  MLQNLGLTVLDQKPYEVTPADGRHFQLYDFGVRLPE----GVDAIGPEDARTEDLIEDTL 654

Query: 678  AATWTGKAENDGFNALVLSAGLTWREAMVLRAYAKYLRQAGSTFSQDYMEDTLRNNVHTT 737
             A  + ++E+D  N LVL+  LTWR   VLR+Y +YL Q G + S DY+ DTL      T
Sbjct: 655  CAVLSNRSESDSLNRLVLTERLTWRTVAVLRSYVRYLLQLGHSNSFDYIADTLLAFPAVT 714

Query: 738  RLLINLFEARMAPERQRAGREIV-DALLEEVDAALDQVASLDEDRILRSFLTVIKATLRT 796
            R L+  F+A   P    A R    DA    +  ALD+V +LD D++LR+   ++ AT+RT
Sbjct: 715  RGLVEFFDASFNPALDDAVRGSQRDAAQTRLMEALDEVPTLDADKLLRALTEIMAATVRT 774

Query: 797  NFFQEASGGVPHDYVSMKFDPQAIPDLPAPRPAFEIWVYSPRVEGVHLRFGKVARGGLRW 856
            N +Q          ++ K +P  I   P P P FEIWV+SPRVEG HLRFG VARGGLRW
Sbjct: 775  NVYQH------RPTMAFKLNPGRISTAPRPHPMFEIWVWSPRVEGTHLRFGPVARGGLRW 828

Query: 857  SDRREDFRTEILGLVKAQMVKNTVIVPVGAKGGFVAKQLPDPGVDRDAWLAEGIASYKTF 916
            SDRREDFRTE+LGLVKAQMVKN+VIVP GAKGGF  KQLPDP VDRDAW+ EG  +YK F
Sbjct: 829  SDRREDFRTEVLGLVKAQMVKNSVIVPNGAKGGFYPKQLPDPAVDRDAWVREGREAYKLF 888

Query: 917  ISALLDITDNMVAGE-----VVHPADVVRHDEDDTYLVVAADKGTAKFSDIANEVAESYN 971
            I++LLDITDN+V  E     VVHP  VVR D  D+YLVVAADKGTA FSD AN ++  Y 
Sbjct: 889  IASLLDITDNLVRDETGHDVVVHPEQVVRRDGQDSYLVVAADKGTASFSDTANAISAEYG 948

Query: 972  FWLGDAFASGGSAGYDHKGMGITARGAWESVKRHFRELGVDTQTQDFTVVGIGDMSGDVF 1031
            FWLGDAFASGGS GYDHK MGITARGAWESVKRHF ELGVDTQT+DFTVVG+GDMSGDVF
Sbjct: 949  FWLGDAFASGGSVGYDHKAMGITARGAWESVKRHFFELGVDTQTEDFTVVGVGDMSGDVF 1008

Query: 1032 GNGMLLSEHIRLVAAFDHRHIFIDPTPDAATSYAERRRLFELPRSSWEDYNTELLSAGGG 1091
            GNGMLLSEHIRLVAAFDHR IF+DP PD A SYAER RLF  PRSSW+DY+ E +SAGGG
Sbjct: 1009 GNGMLLSEHIRLVAAFDHRDIFLDPDPDPAVSYAERERLFGRPRSSWQDYDREKISAGGG 1068

Query: 1092 IFPRTAKSIPVNAHVREALGIEPGVTKMTPAELMKAILSSPVDLLWNGGIGTYVKASTES 1151
            ++ RT KS+PV+  VREALG+  GV +MTP EL++AIL++P DLL+NGGIGTYVK+S ES
Sbjct: 1069 VYSRTVKSVPVSPQVREALGLPDGVEEMTPIELIRAILTAPADLLYNGGIGTYVKSSQES 1128

Query: 1152 NADVGDKGNDAIRVDGKDLRVQVVGEGGNLGLTQLGRIEFALQGGRINTDAIDNSAGVDT 1211
            + DVGDK NDAIRVDG DLRV+VVGEGGNLG TQLGR+E AL G  +NTDAIDNS GV++
Sbjct: 1129 HTDVGDKANDAIRVDGADLRVKVVGEGGNLGCTQLGRVEAALGGVLLNTDAIDNSGGVES 1188

Query: 1212 SDHEVNIKILLNGLVKDGDMTVKQRNKLLAQMTDEVGALVLRNNYAQNTAIANALAQSRD 1271
            SD EVNIKIL++ +V  G++  ++R   +  MTDEV  LVL  N AQN  +    +++  
Sbjct: 1189 SDREVNIKILVDRMVVAGELAAEERAGFIEAMTDEVAGLVLETNVAQNVLLTTERSRTAR 1248

Query: 1272 MLHAQQRFMRHLVREGHLNRALEFLPTDRQIRERLSS-GHGLTGPETAVLLAYTKITVAE 1330
               +  RFM  L     L+R +E LP+D ++R+R++  G G+T P  +VL AY KI + E
Sbjct: 1249 FNESYLRFMHWLEENAELDRQIESLPSDEELRQRVTRLGLGITSPGLSVLAAYAKIQLFE 1308

Query: 1331 ELLHTSLPDDPYLKGLLHAYFPTALREQFAEQVDGHPLRREITTTVLVNDTVNTGGTTYL 1390
             L+ + L +DP+   +L  YFP  + ++F   VD HPLR EI  TV+ N  +N GG T++
Sbjct: 1309 ALVDSDLAEDPWFARVLEEYFPAQITDRFGRLVDTHPLRAEIICTVVANRMINYGGVTFV 1368

Query: 1391 HRMREETGASLEEIVRAQTVARAIFRSSPVWDAVEELDTKADAAVQTRIRLHSRRLVERG 1450
             R+ +ETGAS  +I RA   A  I+           L       +  R+ L   R+++R 
Sbjct: 1369 QRVIDETGASPADIARAFVAAVEIYDLEDYVRRHRVLPAGTPVELWDRMFLDMHRVLDRV 1428

Query: 1451 TRWLLNNRPQPLELAETVDFFAERVEQVWSQLPKLLRGADAEWYQHIYDELTGA---GVP 1507
             RWLL+ +     + E ++ +   V+  +  L   L G D+   Q +      A   GVP
Sbjct: 1429 VRWLLHRQETADPVTEVIERYKPTVDIRF--LEDRLLGEDSR--QRVDSRAEAAVRQGVP 1484

Query: 1508 DEPATLVAGFSSVFAALDIVSVADRMG-----------KEPLDVAEVYYDLADRLGVTQL 1556
               AT  +     FA LD+  +A   G           ++   +A+VY++L DR  +  L
Sbjct: 1485 GPLATEWSQLLDAFALLDVARLAHASGTGLDEDGRIDEEQIKTIAKVYFELYDRYRMEGL 1544

Query: 1557 MDRISDLPRDDRWQSMARAAIREDLYAAHAALTADVLAVGNGSSTPEQRFKAWEEKNAAI 1616
            ++RI+DLP++ RWQ +AR A+RED+YA   AL    L       T  ++  AWEE N + 
Sbjct: 1545 LNRITDLPQETRWQVLARMAMREDVYATLVALADRALRA--PGRTAREKVDAWEEANESR 1602

Query: 1617 LGRARTTLEEI----RQSDAFDLSNLSVAMRTMRTLL 1649
            L R R  L EI    R     +L++LSVA+RTMR  L
Sbjct: 1603 LARLREVLGEIEAEGRGEPGTELASLSVALRTMRNAL 1639


Lambda     K      H
   0.318    0.135    0.393 

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: 6303
Number of extensions: 315
Number of successful extensions: 18
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: 1653
Length of database: 1641
Length adjustment: 52
Effective length of query: 1601
Effective length of database: 1589
Effective search space:  2543989
Effective search space used:  2543989
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 (21.7 bits)
S2: 61 (28.1 bits)

This GapMind analysis is from Sep 24 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 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