Alignments for a candidate for gdhA in Methylotuvimicrobium alcaliphilum 20Z

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Methylotuvimicrobium alcaliphilum 20Z

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate WP_014148683.1 MEALZ_RS10840 NAD-glutamate dehydrogenase domain-containing protein

Query= uniprot:G8AE86
         (1618 letters)



>NCBI__GCF_000968535.2:WP_014148683.1
          Length = 1564

 Score =  734 bits (1894), Expect = 0.0
 Identities = 500/1470 (34%), Positives = 751/1470 (51%), Gaps = 99/1470 (6%)

Query: 97   VEIVNDDMPFLVDSVTAELNRQGLTVHLVIHPVVRVKRDADGQLAELYEPAAAPTDAAPE 156
            + IV  ++  +VDS+ A  + Q L   L+ HPV+ VKR                     E
Sbjct: 95   IVIVCRNLTHVVDSLLALQSDQQLPFQLLAHPVLTVKRQG-------------------E 135

Query: 157  SFMHVEVGAVTGAAAL------DQAREGLERVLADVRAAVADWRAMRQQVRAAIVEADCA 210
                +E   ++G   L      +    G++    +   A+ +W     + R A+ E+   
Sbjct: 136  MITGLESNGLSGTKQLLIVLRLEAVDSGIKDAFFERITAIIEWAEALDRDRIALKES--- 192

Query: 211  RAAVPAIIPDDEVDEAKAFLSWADDDHFTFLGYREYRFESGADGADSSLGLVAGSGLGIL 270
               +  +    E  +  A + W +     F+ ++ +R     D  D++  L    G    
Sbjct: 193  ---LLGLNDISEFSQFSALIDWLEQK--AFIPFKSHRLS--VDDQDTTTSLKP-LGSEFC 244

Query: 271  RDDSVT-VFDGLRNYATLPPDVRDFLRNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDAE 329
            RD++ T + D +R    +    RD+    + L V      SP+    P+     K    +
Sbjct: 245  RDNNPTAISDFIRVMQAVL--ARDYPLIIQYLPVR-----SPLIHDQPLIYIGFKHSLPD 297

Query: 330  GRIIGERLVAGLFTSVAYNRSPREIPYLRRKVAEVMELAGFDPQGHDGKALLHILETYPR 389
            G    E    G+F       +   IP+L+RK+ + +         ++   L  I   +P+
Sbjct: 298  GGGFCEYGFFGVFDETEMGGACSNIPFLQRKIEQTLAHHKTPENSYEYLQLKEIFNLFPK 357

Query: 390  DELFQIQVPELLDIAVGIL--HLQERQRLALFVRKDPFERFASCLVYVPRDRYDTTLRRR 447
             +LF +++P+L D+ +  L  +L   + + L V         S L+ VP   Y   +   
Sbjct: 358  VDLFLLEIPQL-DLLIQSLRRYLYRPEGIKLVVLGGFGLESMSALIIVPIHLYSEEIESV 416

Query: 448  IQSILEAAYDGTCTGFTTQLTESVLARLHFIIRTEPGRVPTVDATDLEARLVQASRGWDD 507
            +   L +  D +       +       LHF++R     + T+D   L+  L +  R W  
Sbjct: 417  LLGRLSSNLDSSAELVRKIMLSGPYLGLHFLLRPTAETI-TIDVDQLDRDLNKQIRPWST 475

Query: 508  HLRDALVEAHGEEQGRTLFRRYADAFPTAYREEFNAEAAVFDIERIEKATAQGTLGINLY 567
             L   L  A+G+ +   L+++Y   FP  Y+       A+ DI  IE       + I L 
Sbjct: 476  SLCRTLERAYGKYKACKLWQKYRTVFPPGYQALMPPRHAIKDIGLIESLLDDEPMTIGLL 535

Query: 568  RPLEAEGDELHVKIYHEGRPVP-LSDVLPMLEHMDLKVITEAPFEIAIAGHAAPVWIHDF 626
            RP    G   H +++   R    L + +P+LE+ +L+V+ +  F ++++G   PV+I  F
Sbjct: 536  RPC---GKIRHYRLHFCSRQERYLDEYIPILENFNLRVLDQVQFPLSVSGR--PVFIKSF 590

Query: 627  TARSQNGLPIDCAMVKEKFQDAFAAVWDGRMEDDGFNRLVLRAGLTAREVTVLRAYAKYL 686
            T  +          +K +      AV++G+ E+D  N L++ AG+T +++ VLRAY  Y 
Sbjct: 591  TISAAKSQHDSFTELKSRLLSGIGAVFNGKAENDELNSLLVLAGMTWQQIDVLRAYRNYY 650

Query: 687  RQARIPYGQDVVESTLAGHPAIARKLVALFHSRFDPARRSQNDPGLAAEIERA------- 739
             Q   P         L  + + A  L   F +RF P      DP L   ++R        
Sbjct: 651  LQLGYPTTTSSFNQALLANSSTAFALFEYFEARFRP------DPNLGEPMQREEQLLFPL 704

Query: 740  -------LDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYLSFKIDSRNIDDL 792
                   L GV +++ D+ILR   NL+  T+R N +      R   +++FKI+S  I D+
Sbjct: 705  RLKLLENLSGVTDINHDKILRTLFNLIDATMRCNFHVR--QKRDDFFIAFKINSLGIIDM 762

Query: 793  PLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKNTVIVP 852
            P P+P  E++V++  MEG+HLRGGK++RGGIRWSDR +DFRTE+L LM+ QM KN +I+P
Sbjct: 763  PPPKPQNEIYVHAVDMEGIHLRGGKISRGGIRWSDRPDDFRTEVLDLMQTQMSKNALIIP 822

Query: 853  VGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQGAVVPPPEVVRHD 912
             G+KGGF+VK P      REA    G + Y  L++GLLD+TDN   +  VVP P +V +D
Sbjct: 823  KGAKGGFIVKAPVADPGFREA----GRKAYVKLVQGLLDLTDNY-VEDQVVPLPGIVSYD 877

Query: 913  GDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKKMGITARGAWESV 972
              DPYLVVAADKGTA FSD+ANSVS  + FWLGDAFASGGS GY+HK +GITARGAWE V
Sbjct: 878  DHDPYLVVAADKGTAQFSDLANSVSAQYHFWLGDAFASGGSNGYNHKALGITARGAWECV 937

Query: 973  KRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHRHIFIDPDP-DAA 1031
            KRHFRELG D Q++ FTVVG+G M GDVFGNGMLLS    LLAA   RHIFIDP P D  
Sbjct: 938  KRHFRELGKDIQSEPFTVVGIGSMDGDVFGNGMLLSHSTHLLAAISGRHIFIDPAPADLE 997

Query: 1032 RSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRFGIAKDHVTPLE 1091
            +S+ ER+RLF+LP SSW DYD SL+S GG ++ R AK + ++P++R+  GI    +    
Sbjct: 998  KSYLERKRLFELPGSSWDDYDRSLISEGGGIYSRHAKDIAVSPQLRKWLGIRYKSLDGST 1057

Query: 1092 LMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRAKVIGEGANLGV 1151
            L++ LL A V+LLWFGGIGTY+KA  E + +VGD++ND +R+D   +RA V+GEGANLG 
Sbjct: 1058 LIRLLLTAPVELLWFGGIGTYVKATNEKHEDVGDRSNDDVRVDALQLRAAVVGEGANLGF 1117

Query: 1152 TQRGRIEAAQHGVRLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMTLKQRDQLLAAM 1211
            TQ+ RIE A  G R++TDA+ NS GVD SDHEVN+KILL    ++    LK   +   ++
Sbjct: 1118 TQKARIEFALGGGRIDTDAVHNSGGVDCSDHEVNLKILLTG--LQKKQGLKDYRETFESL 1175

Query: 1212 TDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRAIEYLPDEEELS 1271
            TDEV   VL +NY QS  L++ + +     E    L   LE AG L+RAIE  P  +E+ 
Sbjct: 1176 TDEVCAAVLTNNYKQSLCLSLEQLRVKGNAEQYLLLSERLESAGVLDRAIESFPSYKEVM 1235

Query: 1272 ARMANREGLTRPELAVLLAYAKITLYDDLL-ASDLPDDPFMADDLTRYFPKPLRKAHAEA 1330
             R  + + +TRPE AVL+A  KI L  D++  S+L         L  YFP P+R+  AE 
Sbjct: 1236 GR--SGQIITRPEFAVLMAACKIQLTQDIMDRSELISASDYDIYLQSYFPDPIRQNFAEH 1293

Query: 1331 VGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVRDAFGLRSLWT 1390
            +  H L   I AT ++N+++N+ G  F+       G    D    Y              
Sbjct: 1294 LANHPLAPAIKATVISNTVINQAGCGFL-NWHNDNGGSIIDSITVYLTFDQVLEAADFRR 1352

Query: 1391 GIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQQPLDIARETEAFRPGIETLLAGL 1450
             I  LD ++PA  Q  ++L+    +   + W L +              RP   T L   
Sbjct: 1353 EIFSLDNLIPAEQQYGLLLQLENVLAEFSQWVLMN----------ELVVRPDPIT-LENY 1401

Query: 1451 DNVLDAEETARLTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGRTGRGVADVAA 1510
             + L A     + +   +    GVP +LA+R+A +  L   P +  ++  +G   + V  
Sbjct: 1402 RSCLTAFANEFIPSDSENEAANGVPVKLAKRIAFINALNDFPQIAVLSTESGYAFSTVRK 1461

Query: 1511 VYFMLGRRFGLEWLRDKAAAAKAENHWQKQ 1540
             +  + +   L+ L ++ +A   +NHW+++
Sbjct: 1462 TFVEVAKFLDLDKLLEQLSAITVQNHWERK 1491


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: 4989
Number of extensions: 240
Number of successful extensions: 15
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: 1618
Length of database: 1564
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1513
Effective search space:  2370871
Effective search space used:  2370871
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