Alignments for a candidate for gdhA in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Mycolicibacterium vanbaalenii PYR-1

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate WP_011781225.1 MVAN_RS20390 NAD-glutamate dehydrogenase

Query= BRENDA::A0R1C2
         (1594 letters)



>NCBI__GCF_000015305.1:WP_011781225.1
          Length = 1627

 Score = 2419 bits (6269), Expect = 0.0
 Identities = 1237/1608 (76%), Positives = 1368/1608 (85%), Gaps = 14/1608 (0%)

Query: 1    MIRRLSVAFLSTYRGPQADAPGVTS--TGPLAVAAHDDLVSDDLVAAHYRLASMRAPGET 58
            +I RL  A+L+TYRGP   APG  S  TGPL     D +    LVAAHYRL + R+PG T
Sbjct: 20   VIDRLLPAYLATYRGPHGGAPGAESAVTGPLRRQGTDTVNGPALVAAHYRLGAQRSPGAT 79

Query: 59   KAAVYPGDA--GSGAALQIVTDQAPMLVDSVTVLLHRHGIAYTAIMNPVFRVRRGLDGEL 116
            + AV+  D   G G ALQ+VTD A +L+DS+TVLLHR G+AYTAIMNPVFRVRRG  GEL
Sbjct: 80   RVAVHAADVEGGFGPALQVVTDNAAILMDSITVLLHRIGVAYTAIMNPVFRVRRGAGGEL 139

Query: 117  LDVRPAAEAAPGDGADECWILVPITAAADGEALTEATRLVPGILAEARQIGLDSGAMIAA 176
             D+ PA++A   DG DE W+ V +  + D  AL EA  L+P +LA+ARQ+ LDS  M AA
Sbjct: 140  QDIAPASDATFVDGVDETWVHVQLADSVDRRALAEAEELLPRVLADARQVALDSTGMAAA 199

Query: 177  LHGLANDLATDLEGHFPNAERKEVAALLRWLADGHFVLLGYQQCVVGDGNAEVDPASRLG 236
            L  LA +L +D    FP+ +RK+VAALLRWLADGHFVLLGYQ+C V DG A VDP+SRLG
Sbjct: 200  LRTLAAELDSDPGRRFPSPDRKDVAALLRWLADGHFVLLGYQRCPVRDGEATVDPSSRLG 259

Query: 237  VLRLRNDVLPPLTDSDDLLVLAQATMPSYLRYGAYPYIVVVRESPGAS-----RVIEHRF 291
            VLRLR DV P LT+ D+LL LAQAT+PS+LRYG YP IVVVRE  G +       IEHRF
Sbjct: 260  VLRLREDVFPQLTNKDELLTLAQATIPSFLRYGTYPQIVVVREQSGDADADDAAAIEHRF 319

Query: 292  VGLFTVAAMNANALEIPLISRRVEEALAMAHRDPSHPGQLLRDIIQTIPRPELFALSSKQ 351
            VG+FTVAAMNAN LEIPL+SRRV +ALAMAHRDPSHPGQL+ DIIQTIPR ELFALS++ 
Sbjct: 320  VGMFTVAAMNANVLEIPLVSRRVNDALAMAHRDPSHPGQLVLDIIQTIPRSELFALSARG 379

Query: 352  LLEMALAVVDLGSRRRTLLFLRADHLAHFVSCLVYLPRDRYTTAVRLEMQDILVRELGGA 411
            LL+MA+AVVDLGSRRR LLF+RAD LAHFVSCLVYLPRDRYTTAVRLEMQDILVRELGG 
Sbjct: 380  LLDMAMAVVDLGSRRRALLFMRADPLAHFVSCLVYLPRDRYTTAVRLEMQDILVRELGGV 439

Query: 412  GIDYSARVSESPWAVVHFTVRLPEGTAADSVDTSLENESRIQDLLTEATRNWGDRMISAA 471
             IDY+ARVSESPWAVVHFTVR+PEG+    +D S  NESRIQDLLTEA R W DR++ A 
Sbjct: 440  SIDYAARVSESPWAVVHFTVRMPEGSRPQDIDVSEPNESRIQDLLTEAARTWSDRLLGAV 499

Query: 472  AAAS-ISPAALEHYAHAFPEDYKQAFAPQDAIADISLIEALQDDSVKLVLAD---TAEDR 527
            +A   +  A  EHYA AF E YKQA  P  A+ADI++IE LQD+SVKLVLAD   TAE  
Sbjct: 500  SAGGEVDQATAEHYASAFSEVYKQAIDPVHALADIAVIEELQDNSVKLVLADSDDTAESG 559

Query: 528  VWKLTWYLGGHSASLSELLPMLQSMGVVVLEERPFTLRRTDGLPVWIYQFKISPHPSIPH 587
            V  L WYLGG SASLS LLPMLQSMGVVVLEERPFT+ R DGLPVWIYQFK+SPH  IP 
Sbjct: 560  VSHLNWYLGGRSASLSRLLPMLQSMGVVVLEERPFTVVRPDGLPVWIYQFKVSPHRGIPE 619

Query: 588  APDAEAQRDTAQRFADAVTAIWHGRVEIDRFNELVMRAGLTWQQVVVLRAYAKYLRQAGF 647
            AP    +  TA+RFADAVTAIWHG  EIDRFNELV+RA LTWQQV VLRAYA+YL+QAGF
Sbjct: 620  APPGPQREATAERFADAVTAIWHGNAEIDRFNELVLRAELTWQQVAVLRAYARYLKQAGF 679

Query: 648  PYSQSHIESVLNENPHTTRSLIDLFEALFDPSQETDG-RRDAQGAAAAVAADIDALVSLD 706
             YSQSHIESVLN+N  T RSLI LFEALF P ++  G  RDAQ AAAAVAADIDALVSLD
Sbjct: 680  AYSQSHIESVLNDNAGTARSLIALFEALFRPVEQGPGANRDAQAAAAAVAADIDALVSLD 739

Query: 707  TDRVLRAFANLIEATLRTNYFVARPDSARARNVLAFKLNPLVIKELPLPRPKFEIFVYSP 766
            TDRVLRAFA++I+ATLRTNYF+   +SARARNVL+ KLNP +I ELPLPRPKFEIFVYSP
Sbjct: 740  TDRVLRAFASMIQATLRTNYFITGQESARARNVLSLKLNPQLIDELPLPRPKFEIFVYSP 799

Query: 767  RVEGVHLRFGFVARGGLRWSDRREDFRTEILGLVKAQAVKNAVIVPVGAKGGFVVKRPPT 826
            RVEGVHLRFGFVARGGLRWSDRREDFRTEILGLVKAQAVKNAVIVPVGAKGGFVVK PP 
Sbjct: 800  RVEGVHLRFGFVARGGLRWSDRREDFRTEILGLVKAQAVKNAVIVPVGAKGGFVVKHPPA 859

Query: 827  LTGDAAADREATRAEGVECYRLFISGLLDVTDNVDKATGAVVTPPEVVRRDGEDAYLVVA 886
             TGDAAADR+ATR EGV CYRLFI+GLLD+TDNVDK TG +V P +VVRRDG+DAYLVVA
Sbjct: 860  PTGDAAADRDATREEGVACYRLFIAGLLDITDNVDKVTGGIVAPADVVRRDGDDAYLVVA 919

Query: 887  ADKGTATFSDIANEVAKSYGFWLGDAFASGGSIGYDHKAMGITAKGAWESVKRHFREMGV 946
            ADKGTATFSDIAN+VAKSYGFWLGDAFASGGS+GYDHKAMGITAKGAWESVKRHFREMGV
Sbjct: 920  ADKGTATFSDIANDVAKSYGFWLGDAFASGGSVGYDHKAMGITAKGAWESVKRHFREMGV 979

Query: 947  DTQTQDFTVVGIGDMSGDVFGNGMLLSKHIRLVAAFDHRDIFLDPNPDAGRSWDERKRLF 1006
            DTQ++DFTVVG+GDMSGDVFGNGMLLSKHIRL+AAFDHR IF+DP PDA  SW+ERKRLF
Sbjct: 980  DTQSEDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHRHIFIDPTPDAASSWEERKRLF 1039

Query: 1007 DLPRSSWADYDKSLISEGGGVYSRQQKSIPISPQVRTALGLDADVEELTPPALIKAILKA 1066
            +LPRSSW DYD SLIS GGGVYSR+QKSIP+S Q R ALGLD  V +LTPPAL+KAILKA
Sbjct: 1040 ELPRSSWEDYDTSLISPGGGVYSREQKSIPVSAQARAALGLDDQVTDLTPPALMKAILKA 1099

Query: 1067 PVDLLWNGGIGTYIKAETEADADVGDRANDQIRVCGNQVRAKVIGEGGNLGVTALGRIEF 1126
            P DLLWNGGIGTY+KAETEADADVGDRAND +RV GN+VRAKVIGEGGNLGVT+ GR EF
Sbjct: 1100 PADLLWNGGIGTYVKAETEADADVGDRANDAVRVNGNEVRAKVIGEGGNLGVTSRGRTEF 1159

Query: 1127 DLAGGRINTDALDNSAGVDCSDHEVNIKILIDSAVTAGKVTPEERTELLLSMTDEVGELV 1186
            DL GGRINTDA+DNSAGVDCSDHEVNIKILIDS VTAGKV    R+ LL SMTDEVG LV
Sbjct: 1160 DLCGGRINTDAMDNSAGVDCSDHEVNIKILIDSLVTAGKVEESGRSALLSSMTDEVGRLV 1219

Query: 1187 LADNRDQNDLMGTSRANAASLLSVHARMIKDLVDNRGLNRELEALPSEKEIRRRADAGIG 1246
            LADN  QNDLMGTSRANAASLL+VH RMI+  V+ RGLNRELEALPSEKEIRRR +AGIG
Sbjct: 1220 LADNESQNDLMGTSRANAASLLNVHGRMIRSFVEERGLNRELEALPSEKEIRRREEAGIG 1279

Query: 1247 LTSPELATLMAHVKLALKDDVLASDLPDQEVFASRLPYYFPTRLREELHGEIRSHQLRRE 1306
            LTSPELATLMAHVKLALKDD+LA DLPDQEVFASRLP YFP  LR++   EIR+HQLRRE
Sbjct: 1280 LTSPELATLMAHVKLALKDDLLAGDLPDQEVFASRLPSYFPATLRDQFSPEIRAHQLRRE 1339

Query: 1307 IITTMLVNDLVDTAGISYAYRITEDVGVGPVDAVRSYVAINAIFGIGDVWRRIRAAGDAG 1366
            I+TTMLVND+VDTAGISYAYR+TEDVGV PVDAVRS+VA +AIFG+G VWR+IR AG  G
Sbjct: 1340 IVTTMLVNDVVDTAGISYAYRVTEDVGVAPVDAVRSFVAADAIFGVGRVWRQIREAGANG 1399

Query: 1367 VPTSVTDRMTLDLRRLVDRAGRWLLNYRPQPLAVGAEINRFGAKVAALTPRMSEWLRGDD 1426
            VP +VTDRMTLDLRRL+DRA RWLLNYRPQPLAVGAEINRF  KVAALTPRM +WLRGDD
Sbjct: 1400 VPVAVTDRMTLDLRRLIDRAARWLLNYRPQPLAVGAEINRFADKVAALTPRMPDWLRGDD 1459

Query: 1427 KAIVSKEAGDFASHGVPEDLAYHIATGLYQYSLLDVIDIADIVDREPDEVADTYFALMDH 1486
            KAIV+KEA +F+S GVP+D+AY +A+GLYQ+SLLDVIDIADIVDR+P EVAD YFALMDH
Sbjct: 1460 KAIVAKEAAEFSSQGVPDDVAYMVASGLYQFSLLDVIDIADIVDRDPAEVADAYFALMDH 1519

Query: 1487 LGADALLTAVSRLSRDDRWHSLARLAIRDDIYGSLRALCFDVLAVGEPDENGEEKIAEWE 1546
            LG D LLTAVSRLSR DRWHSLARLAIRDDIYGSLRALCFDVLAVGEPDE+G EKIAEWE
Sbjct: 1520 LGTDGLLTAVSRLSRYDRWHSLARLAIRDDIYGSLRALCFDVLAVGEPDEDGVEKIAEWE 1579

Query: 1547 TTNSSRVTRARRTLTEIYKDGEQDLATLSVAARQIRSMTRTSGTGTTG 1594
            TTNSSRV+RARRTL E+Y+ GE DLATLSVAARQIRSMTRTSGTG++G
Sbjct: 1580 TTNSSRVSRARRTLAELYESGEHDLATLSVAARQIRSMTRTSGTGSSG 1627


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: 6370
Number of extensions: 248
Number of successful extensions: 8
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: 1627
Length adjustment: 51
Effective length of query: 1543
Effective length of database: 1576
Effective search space:  2431768
Effective search space used:  2431768
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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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 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