GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Sphingomonas koreensis DSMZ 15582

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate Ga0059261_1252 Ga0059261_1252 NAD-specific glutamate dehydrogenase

Query= uniprot:G8AE86
         (1618 letters)



>FitnessBrowser__Korea:Ga0059261_1252
          Length = 1537

 Score = 1015 bits (2624), Expect = 0.0
 Identities = 625/1535 (40%), Positives = 849/1535 (55%), Gaps = 69/1535 (4%)

Query: 89   GWQSHRTVVEIVNDDMPFLVDSVTAELNRQGLTVHLVIHPVVRVKRDADGQLAELYEPAA 148
            G  S    + +VNDDMPFLVDS++A +    + +  VIHPVV V+R  DG L  +     
Sbjct: 61   GEDSRTMRLAVVNDDMPFLVDSISATIAAHDIAIRRVIHPVVAVERTGDGALTGI----- 115

Query: 149  APTDAAPESFMHVEVGAVTGAAALDQAREGLERVLADVRAAVADWRAMRQQVRAAIVEAD 208
                 + ES +++E+            R+ LER L  VRAAV DW  +R+ +       D
Sbjct: 116  -GAGGSRESMVYMELERADARDRTGLVRD-LERNLGHVRAAVTDWPELRRAM-----SDD 168

Query: 209  CARAAVPAIIPDDEVDEAKAFLSWADDDHFTFLGYREYRFESGADGADSSLGLVAGSGLG 268
             +R   P         E  + L W      T +G+  +  +     A         +G+ 
Sbjct: 169  ASRVGDP---------EGASLLRWFQGGSMTLVGHEVWHIDGSVTDA---------AGIC 210

Query: 269  ILRDDSVTVFDGLRNYATLPPDVRDFLRNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDA 328
             ++ D+  + D  R  A     V  F +  +  ++ K N  S VHR  P+D  L+   + 
Sbjct: 211  RMKLDTPLLADASRQLA-----VEWFEKGGQPPLLLKSNLISTVHRRAPLDLVLVPLREG 265

Query: 329  EGRIIGERLVAGLFTSVAYNRSPREIPYLRRKVAEVMELAGFDPQGHDGKALLHILETYP 388
             G++ G  + AGL+TS A + +P E+P LR ++  +    GFDP+GH GKAL H L   P
Sbjct: 266  -GKVTGLSIHAGLWTSAALHSTPDEVPLLRARLTSLETKFGFDPRGHTGKALTHALTGLP 324

Query: 389  RDELFQIQVPELLDIAVGILHLQERQRLALFVRKDPFERFASCLVYVPRDRYDTTLRRRI 448
             D         L  IA+  + + +R R  L + +    R     V++PRD   T  R  I
Sbjct: 325  HDLTIAFPQEALEQIALTAMSVTDRPRSKLVLIRSALGRHLFAFVWLPRDDVSTGRRVAI 384

Query: 449  QSILEAAYDGTCTGFTTQLTESVLARLHFIIRTE-PGRVPTVDATDLEARLVQASRGWDD 507
              +LE + + T   ++  L +  +A L + +     GR+P  DA  L+A L +  RGW  
Sbjct: 385  GEMLERSANATQISWSIALEDGPVALLRYTLDLRGEGRMP--DAAALDAELERMVRGWLP 442

Query: 508  HLRDALVE-AHGEEQGRTLFRRYADAFPTAYREEFNAEAAVFDIERIEKATAQGTLGINL 566
             +  AL+E      +   +  R+A AFP  YR     E A  DI RI          +  
Sbjct: 443  AVEAALIEDGLAANRAARMALRHAPAFPPGYRNHNGPEEAARDIVRIAGLADADARSVRF 502

Query: 567  YRPLEAEGDELHVKIYHEGRPVPLSDVLPMLEHMDLKVITEAPFEIAIAGHAAPVWIHDF 626
            +     +  +L +K+Y  G  + LSD +P+ E+   +VI E P   A++G     +IHDF
Sbjct: 503  FE----QAGKLRIKLYRLGGALALSDAVPVFENFGFRVIEELP--TALSGETG-AYIHDF 555

Query: 627  TAR--SQNGLPIDCAMVKEKFQDAFAAVWDGRMEDDGFNRLVLRAGLTAREVTVLRAYAK 684
                  +  L  D   V+E    A AAV +GR E+D FNRL++ AG+    V +LRA+ +
Sbjct: 556  EVELTGEAKLKGDIPTVEE----AIAAVLEGRAENDAFNRLIVEAGIAPASVVLLRAWFR 611

Query: 685  YLRQARIPYGQDVVESTLAGHPAIARKLVALFHSRFDPARRSQNDPGLA---AEIERALD 741
            YLRQ  + YG   V   L   PA+A  LV  F +  DPAR   +   +    A I   LD
Sbjct: 612  YLRQTGLTYGLVTVVEALRRAPAVATALVERFAAAHDPARAKGSAEAVKTADAAIAAGLD 671

Query: 742  GVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYLSFKIDSRNIDDLPLPRPMVEV 801
             V  +D+DRILR    ++  TLRTNA+   A       L+FK+DS  + +LP P P  E+
Sbjct: 672  AVSAIDDDRILRAIAGVIRATLRTNAFAPAA----AEALAFKLDSARVPNLPAPLPWREI 727

Query: 802  FVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKNTVIVPVGSKGGFVV 861
            +VYSPR+EG+HLR G VARGG+RWSDRR+DFRTEILGLMKAQ VKN VIVP G+KGGF  
Sbjct: 728  WVYSPRVEGIHLRAGPVARGGLRWSDRRDDFRTEILGLMKAQRVKNAVIVPTGAKGGFYP 787

Query: 862  KRPPPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQGAVVPPPEVVRHDGDDPYLVVA 921
            K+ P P+  R+A   EG E Y+  +R LL ITDN+   G VV P  V   DG+DPY VVA
Sbjct: 788  KQLPSPAIDRDAWFEEGKESYRIFIRSLLSITDNI-VSGKVVHPDSVAILDGEDPYFVVA 846

Query: 922  ADKGTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKKMGITARGAWESVKRHFRELGH 981
            ADKGTATFSD+AN+++++  FWLGDAFASGGS GYDHK MGITA+GAW SV+RHF E+G 
Sbjct: 847  ADKGTATFSDVANAIAIERNFWLGDAFASGGSVGYDHKAMGITAKGAWVSVQRHFLEMGT 906

Query: 982  DTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHRHIFIDPDPDAARSWEERQRLF 1041
            D QTQ   V G GDMSGDVFGNGMLLSK I+L+AAFDHRHIF+DPDPD A+SW+ER R+F
Sbjct: 907  DVQTQSIRVAGCGDMSGDVFGNGMLLSKAIKLVAAFDHRHIFLDPDPDPAKSWDERARMF 966

Query: 1042 DLPRSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRFGIAKDHVTPLELMQTLLKAEV 1101
             L RSSWADYD SL+S GG VF R+ K ++L+P++R+  GI  + + P  L+  +LKA V
Sbjct: 967  ALSRSSWADYDPSLISKGGGVFARTEKVIKLSPQVREVLGIDAEEMEPNALISAILKAPV 1026

Query: 1102 DLLWFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRAKVIGEGANLGVTQRGRIEAAQ 1161
            DL+WFGGIGTY+KAA E + EVGD AND LR++  D+RA+ IGEGANLGVTQ  RI  + 
Sbjct: 1027 DLIWFGGIGTYVKAASEAHIEVGDPANDRLRVNAEDMRARAIGEGANLGVTQAARIAFSL 1086

Query: 1162 HGVRLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMTLKQRDQLLAAMTDEVAGLVLA 1221
             G RLNTD IDNSAGVD SD+EVNIKI LN  V+ G + +  R+ LLA+MTD+VA LVL 
Sbjct: 1087 RGGRLNTDFIDNSAGVDCSDNEVNIKIALNREVIEGRLKIDDRNTLLASMTDDVAHLVLE 1146

Query: 1222 DNYLQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRAIEYLPDEEELSARMANREGLT 1281
            DN LQ+ AL+     G  A+ +  R+I  LE +GRL+RA+E L   E+   R     GLT
Sbjct: 1147 DNRLQTLALSFLENDGAVAVPSFVRVIEILEASGRLDRAVEGLGSNEDYLRRAQEGRGLT 1206

Query: 1282 RPELAVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFPKPLRKAHAEAVGRHRLRREII 1341
            RPELAVLLA +K+ L D +   DL  DP +  DL   FP  ++K   + +  HRLR EI+
Sbjct: 1207 RPELAVLLATSKLALQDAIEDGDLGLDPELEPDLIAAFPPAMQKKFKKPIEEHRLRGEIV 1266

Query: 1342 ATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVRDAFGLRSLWTGIEDLDTVVPA 1401
            AT + N +VNR G     E+ E+ G    D+A  + +    FGL ++W  IE       A
Sbjct: 1267 ATKLANRIVNRLGVLHPFELAEEEGASLRDIAAMFVVAERLFGLPAIWEAIETAAISEQA 1326

Query: 1402 ALQTSMILETVRHMERAAAWFLASCQQPLDIARETEA-FRPGIETLLAGLDNVLDAEETA 1460
             L    +L+ V    RA    L    +P +   E  A  +PGI  L      +L  E  A
Sbjct: 1327 RL---ALLDEVAVATRAQIADLLRVDRPDEGPGELIARLKPGIAGLDRQTKKLLKEEARA 1383

Query: 1461 RLTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGRTGRGVADVAAVYFMLGRRFG 1520
            +     A  +E G P +L  ++  +  L  A  L  +  R G    ++   +  LG+  G
Sbjct: 1384 QSGRIAAKLEEAGAPHDLVTKIVRIFELDGAVGLADLGQRRGIDETELTHAFTHLGQELG 1443

Query: 1521 LEWLRDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRVLEAVDQLPAEAPVEAWIAHR 1580
            L+W +  AA   A + W++  +A L  D       L    L   D     A V+AW+A  
Sbjct: 1444 LDWAQAVAARIVAGDPWERLLIAGLARDF----QQLRLEFLARADGKDPRAAVDAWLADH 1499

Query: 1581 RPVVERVEQLLSELRTQPNVDLSMLAVANRQLRGL 1615
               VE+   L++  R  P  + +MLA    Q R L
Sbjct: 1500 GARVEQFAALVARARKAPTPNAAMLAQIAGQARVL 1534


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: 5596
Number of extensions: 270
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: 1537
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1486
Effective search space:  2328562
Effective search space used:  2328562
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