GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Williamsia sterculiae CPCC 203464

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_076480672.1 BW971_RS14270 NAD-glutamate dehydrogenase

Query= BRENDA::A0R1C2
         (1594 letters)



>NCBI__GCF_900156495.1:WP_076480672.1
          Length = 1591

 Score = 1432 bits (3708), Expect = 0.0
 Identities = 791/1573 (50%), Positives = 1027/1573 (65%), Gaps = 58/1573 (3%)

Query: 43   VAAHYRLASMRAPGETKAAVYPGDAGSGAALQIVTDQAPMLVDSVTVLLHRHGIAYTAIM 102
            V+ H  +A+ R+PGE    V     GS   +  VTD  P LV+ V+  L R G++   I 
Sbjct: 48   VSHHLSVAAQRSPGEVLVEVRAAARGS-ITVTTVTDDMPRLVEGVSSALGRLGLSVWRID 106

Query: 103  NPVFRVRRGLDGELLDVRP---AAEAAPGDGADECWILVPITAAADGEALTEATR-LVPG 158
            +PV  V R   G+LL +     A    PG+   E WI V       G     A R  V  
Sbjct: 107  HPVLSVWRDAAGQLLAIGTPDSADNGEPGERIAESWIHVEAQPIRPGSVDAPAVRDRVAE 166

Query: 159  ILAEARQIGLDSGAMIAALHGLANDLATDLEGHFPNAERKEVAALLRWLADGHFVLLGYQ 218
            ++     +  D  AM   L  +A+    D  G +P        ALLRW+A G F  +G+ 
Sbjct: 167  VIGRVVDVHRDHRAMTERLRTVADRCGADA-GQYP--------ALLRWMAGGMFAPIGWY 217

Query: 219  QCVVGDGNAEVDPASRLGVLRLRNDVLPPLTDSDDLLVLAQATM-----PSYLRYGAYPY 273
                  G  E   A+  GV R  +    P  D D ++   Q  +     P+ +    YP 
Sbjct: 218  TVDQITGAPE---AAGQGVWRSPDF---PRPDRDAVVTAEQPLIRRIHFPTAILRTDYPT 271

Query: 274  IVVVRE-SPGASRVIEHRFVGLFTVAAMNANALEIPLISRRVEEALAMAHRD-PSHPGQL 331
            ++ V E     + V EH F+G+ T  A++ N LEIP++  RV +ALA+A  D  S+ GQ 
Sbjct: 272  LLQVAEVDDTGAPVREHVFIGVLTPTALHENVLEIPVVRERVADALAVAGADIDSYSGQA 331

Query: 332  LRDIIQTIPRPELFALSSKQLLEMALAVVDLGSRRRTLLFLRADHLAHFVSCLVYLPRDR 391
            + +++Q  P  E+FA  + QL     +V+D     R  +FLR+D  A  +S L+YLPRD+
Sbjct: 332  MLELLQGYPLSEIFASDAGQLAANLRSVLDAVPGGRLRVFLRSDPHAETLSALIYLPRDK 391

Query: 392  YTTAVRLEMQDILVRELGGAGIDYSARVSESPWAVVHFTVRLPEGTAADSVDTSLENESR 451
            Y T  R +MQ +L  E G   I+Y+ RVS +  A++H  +R+P   AA   D + E + R
Sbjct: 392  YNTRTRQQMQTLLRDEFGSEDIEYTVRVSVAAHALLHLLMRVP---AATGDDIAPEVQRR 448

Query: 452  IQDLLTEATRNWGDRMI--------SAAAAASISPAALEHYAHAFPEDYKQAFAPQDAIA 503
            +QD L  A+R W D +         + + +A + P  + HY  +  + YK+   P  A+A
Sbjct: 449  LQDALVAASRGWDDGLRELVDAGVQAGSTSAPVGPETIGHYIRSLGDGYKEERDPAAALA 508

Query: 504  DISLIEALQDDSVKLVLADTAEDRVWKLTWYLGGHSASLSELLPMLQSMGVVVLEERPFT 563
            DI+ +  L      + L     D VW+   YL G SA+L+++LP+LQS+GV VL+ERPF 
Sbjct: 509  DITRLATLAPGDFSVDLRRV--DDVWRFGLYLCGRSATLTDVLPVLQSLGVDVLDERPFE 566

Query: 564  LRRTDGLPVWIYQFKISPHPSI-----PHAPDAEAQRDTAQRFADAVTAIWHGRVEIDRF 618
            + R DG    IY+F +SP   +     P  P A A      R  +A +A+W G   +D F
Sbjct: 567  VTRPDGERCRIYEFGLSPTSGMVIHDGPAQPGAGA---VETRVTEAFSAVWRGHAAVDSF 623

Query: 619  NELVMRAGLTWQQVVVLRAYAKYLRQAGFPYSQSHIESVLNENPHTTRSLIDLFEALFDP 678
            NELV+R GL W+Q  +LR+YA+YLRQ GF YS SH+ SVL  +    R L++LF   FDP
Sbjct: 624  NELVLRCGLDWRQAAMLRSYARYLRQCGFAYSASHVASVLGAHADICRGLVELFFGSFDP 683

Query: 679  SQETDGRRDAQGAAAAVAADIDALVSLDTDRVLRAFANLIEATLRTNYFVARPDSARARN 738
                + RR  QG  A +   +  +VSLD DR++ AF  +I AT+RTN+FV  PD    R 
Sbjct: 684  DGADEDRR--QGVVADLDEMVGDIVSLDADRIVSAFVAMIGATVRTNFFVTDPDDGGHRP 741

Query: 739  VLAFKLNPLVIKELPLPRPKFEIFVYSPRVEGVHLRFGFVARGGLRWSDRREDFRTEILG 798
            VL+FKL P  I + P PRP +EIFVYSPR+EGVHLRFG VARGGLRWSDRR+D+RTEILG
Sbjct: 742  VLSFKLRPRDIPQTPQPRPLYEIFVYSPRIEGVHLRFGSVARGGLRWSDRRDDYRTEILG 801

Query: 799  LVKAQAVKNAVIVPVGAKGGFVVKRPPTLTGDAAADREATRAEGVECYRLFISGLLDVTD 858
            LVKAQAVKNAVIVPVGAKGGFVVKRPP  TGD A DR+A R EG+ CYR FI GLLD+TD
Sbjct: 802  LVKAQAVKNAVIVPVGAKGGFVVKRPPAATGDPAVDRDAFRQEGIACYRRFIGGLLDITD 861

Query: 859  NVDKATGAVVTPPEVVRRDGEDAYLVVAADKGTATFSDIANEVAKSYGFWLGDAFASGGS 918
            N+D++TG V+    VVRRDG+D YLVVAADKGTATFSDIAN+VA  Y FWLGDAFASGGS
Sbjct: 862  NLDRSTGEVLPARSVVRRDGDDTYLVVAADKGTATFSDIANDVAAGYDFWLGDAFASGGS 921

Query: 919  IGYDHKAMGITAKGAWESVKRHFREMGVDTQTQDFTVVGIGDMSGDVFGNGMLLSKHIRL 978
             GYDHK MGITA+GAWE+V+RHFREMGVDTQ++DF VVG+GDMSGDVFGNGMLLSKHIRL
Sbjct: 922  AGYDHKVMGITARGAWEAVRRHFREMGVDTQSEDFAVVGVGDMSGDVFGNGMLLSKHIRL 981

Query: 979  VAAFDHRDIFLDPNPDAGRSWDERKRLFDLPRSSWADYDKSLISEGGGVYSRQQKSIPIS 1038
            VAAFDHR +F+DP+PDA  S+ ER+RLFDLPRSSWADYD +LIS GGGV+SR  KSIPIS
Sbjct: 982  VAAFDHRHVFIDPDPDAATSYVERRRLFDLPRSSWADYDPALISTGGGVWSRDLKSIPIS 1041

Query: 1039 PQVRTALGLDADVEELTPPALIKAILKAPVDLLWNGGIGTYIKAETEADADVGDRANDQI 1098
             Q+R ALGLD  V  L+PP L++AIL APVDLLWNGGIGTY+KA  E++ DVGD+AND I
Sbjct: 1042 AQIRAALGLDDGVTALSPPDLMRAILTAPVDLLWNGGIGTYVKASGESNDDVGDKANDAI 1101

Query: 1099 RVCGNQVRAKVIGEGGNLGVTALGRIEFDLAGGRINTDALDNSAGVDCSDHEVNIKILID 1158
            RV G+QVRAKVIGEGGNLGVTA GRIEFDL+GGR+NTDA+DNSAGVDCSDHEVNIKIL+D
Sbjct: 1102 RVNGDQVRAKVIGEGGNLGVTARGRIEFDLSGGRVNTDAMDNSAGVDCSDHEVNIKILLD 1161

Query: 1159 SAVTAGKVTPEERTELLLSMTDEVGELVLADNRDQNDLMGTSRANAASLLSVHARMIKDL 1218
            + V++G +   +R  LL SMTDEVG+LVLADN  QN  +G +RA A   + VH R++++L
Sbjct: 1162 AQVSSGALAAADRNPLLESMTDEVGDLVLADNISQNAELGLARAGAGQSVDVHVRLLREL 1221

Query: 1219 VDNRGLNRELEALPSEKEIRRRADAG-----IGLTSPELATLMAHVKLALKDDVLASDLP 1273
                G++ ELEALP+   +R+R  A       GLTSPELAT++AHVKL LK D+L+++LP
Sbjct: 1222 AGTYGVDLELEALPTVAALRKRVAASDSSRPSGLTSPELATVLAHVKLGLKSDLLSTELP 1281

Query: 1274 DQEVFASRLPYYFPTRLREELHGEIRSHQLRREIITTMLVNDLVDTAGISYAYRITEDVG 1333
            D EVF  RL  YFP  LRE     I  H+LRR+I+TT LVND+VD AGI++A+R+ E   
Sbjct: 1282 DGEVFGPRLHAYFPLPLRERFAEGIAEHRLRRQIVTTSLVNDVVDKAGITHAFRLAEGAM 1341

Query: 1334 VGPVDAVRSYVAINAIFGIGDVWRRIRAAGDAGVPTSVTDRMTLDLRRLVDRAGRWLLNY 1393
              P+D VR+YV ++ +F + D+W RI A  D GV     D M    RRL+ RA RW+L  
Sbjct: 1342 CSPIDVVRAYVVVSTVFALDDLWARIEAV-DGGV--VAIDEMMTYTRRLLFRASRWMLAN 1398

Query: 1394 RPQPLAVGAEINRFGAKVAALTPRMSEWLRGDDKAIVSKEAGDFASHGVPEDLAYHIATG 1453
            RPQPL + AEI R+  +V  L+PR+  WL    +A V+     + + GV E LA      
Sbjct: 1399 RPQPLPIAAEITRYARRVQDLSPRVPGWLGPGSRADVATRVDAWVADGVDESLAADAGVS 1458

Query: 1454 LYQYSLLDVIDIADIVDREPDEVADTYFALMDHLGADALLTAVSRLSRDDRWHSLARLAI 1513
            L+++ LLD+ID A+I DR+  EV + YF ++D LG + LLTAVSRL R DRWH+LARLA+
Sbjct: 1459 LHRFCLLDIIDAAEIADRDEIEVGELYFTVLDDLGVEGLLTAVSRLDRGDRWHALARLAL 1518

Query: 1514 RDDIYGSLRALCFDVLAVGEPDENGEEKIAEWETTNSSRVTRARRTLTEIYKDGEQDLAT 1573
            RDD++  +R+LC  ++ VGEP E+  ++I+EW+T ++SR+ R R  L +I + G+ DLAT
Sbjct: 1519 RDDLHAVVRSLCLQIMEVGEPGESPRQQISEWQTHHASRLARVRAVLDDIAETGDYDLAT 1578

Query: 1574 LSVAARQIRSMTR 1586
            LSVAARQ+RS+ R
Sbjct: 1579 LSVAARQLRSVIR 1591


Lambda     K      H
   0.319    0.136    0.395 

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: 6290
Number of extensions: 313
Number of successful extensions: 12
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: 1594
Length of database: 1591
Length adjustment: 51
Effective length of query: 1543
Effective length of database: 1540
Effective search space:  2376220
Effective search space used:  2376220
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 24 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