Alignments for a candidate for gdhA in Pandoraea thiooxydans ATSB16

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Pandoraea thiooxydans ATSB16

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate WP_047215060.1 PATSB16_RS15970 NAD-glutamate dehydrogenase

Query= uniprot:G8AE86
         (1618 letters)



>NCBI__GCF_001931675.1:WP_047215060.1
          Length = 1639

 Score = 1555 bits (4026), Expect = 0.0
 Identities = 853/1633 (52%), Positives = 1071/1633 (65%), Gaps = 35/1633 (2%)

Query: 4    RAEQLKDELTEEVVRQVRERLGRSRAAPAERFVRQFYDNVPPDDIIQAPAEQLYGAALAM 63
            R+E    +  EE     RER G + AA  E F+R ++     DD++      LYGAA+A 
Sbjct: 5    RSEDKVAQRLEEAAAFARERDGAAPAA-FEAFLRHYFSQADADDVMSRAVPDLYGAAMAH 63

Query: 64   WQWGQQREATDRAKVRVYNPRVEEHGWQSHRTVVEIVNDDMPFLVDSVTAELNRQGLTVH 123
            WQ  Q   + + A++RVYNP VE+ GW    TVVEIVNDDMPFLVDSVT E+NR GL +H
Sbjct: 64   WQLAQTFPSGN-ARIRVYNPDVEQSGWYCEHTVVEIVNDDMPFLVDSVTTEINRLGLALH 122

Query: 124  LVIHPVVRVKRDADGQLAELYEPAA---------APTDAAP-ESFMHVEVGAVTGAAALD 173
               HPV RV RD DGQ       +          AP DA   ES++H+EV   T AA L 
Sbjct: 123  SAFHPVFRVWRDVDGQRRRAAPSSTPNREEASGGAPADAGRLESYIHLEVDRCTEAARLQ 182

Query: 174  QAREGLERVLADVRAAVADWRAMRQQVRAAIVEADCA-RAAVPAIIPDDEVDEAKAFLSW 232
                G+ +VL DVRAAV DW  MR   + A+       RAA  A    +E+ EA+AFL+W
Sbjct: 183  ALHAGIAKVLGDVRAAVEDWPQMRSAAQQAVAALSARERAAGRAPDEGEEIAEARAFLAW 242

Query: 233  ADDDHFTFLGYREYRFESGADGADSSLGLVAGSGLGILRDDSVTVFDGLRNYATLPPDVR 292
              DDHFTFLG R+Y+  S  +     L      GLGILR+       G      L P+  
Sbjct: 243  MIDDHFTFLGQRDYQLVS--EQGTYYLQPDQSPGLGILRE--ALRAPGAAERTALAPEAV 298

Query: 293  DFLRNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPR 352
              + +   + +TK N  + VHR   +D   +K FDA G++ GER   GL+TS AY     
Sbjct: 299  RVIEDASPIFLTKANSRATVHRPGYLDYVGVKLFDAAGKVCGERRFLGLYTSSAYMEPTG 358

Query: 353  EIPYLRRKVAEVMELAGFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQE 412
            EIP +RRKVA V++ AGF P+GH  K+L  ILE YPRDELFQI    L +IA+GIL LQE
Sbjct: 359  EIPLVRRKVAAVVQRAGFLPKGHLAKSLQTILEQYPRDELFQIDSDTLFEIAMGILRLQE 418

Query: 413  RQRLALFVRKDPFERFASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVL 472
            RQR  LFVR+D F+RF SCLV+VPR++++T LR RIQ +L+ AY G+   FT  L+ES+L
Sbjct: 419  RQRTRLFVRRDRFDRFVSCLVFVPREKFNTDLRLRIQQLLQTAYQGSGVEFTPLLSESML 478

Query: 473  ARLHFIIRTEPGRVPTVDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADA 532
            AR+H  +RTEPG+VP VD  DLEAR+VQA+R W D L DAL+E  GEEQG  L  RY  +
Sbjct: 479  ARIHITVRTEPGQVPEVDVRDLEARIVQAARRWQDELADALLERCGEEQGNRLLHRYGGS 538

Query: 533  FPTAYREEFNAEAAVFDIERIEKATAQ-----GTLGINLYRPLEAEGDELHVKIYHEGRP 587
            FP  +RE++ A  AV DI+ +E+  +Q     G L ++LYRP+EA    L  KIY  GRP
Sbjct: 539  FPAGFREDYAARGAVHDIQLMEQIVSQAGARDGALAMHLYRPIEAPPGTLRFKIYQVGRP 598

Query: 588  VPLSDVLPMLEHMDLKVITEAPFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQD 647
            + LS  LPMLEH+ + V  E P+ I     A P+WIHDF  +S +G  +D   +K  F++
Sbjct: 599  IALSRSLPMLEHLGVLVNEERPYRIE-PHDAEPIWIHDFGMQSADGAEVDLTHIKPLFEE 657

Query: 648  AFAAVWDGRMEDDGFNRLVLRAGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPA 707
            AFA +W G  E+DG NRLVLRAGL   EV +LRAYA+Y+RQ    +    +E  L G+PA
Sbjct: 658  AFARIWAGDAENDGLNRLVLRAGLKWPEVRILRAYARYMRQIGSTFSDAYMERALTGNPA 717

Query: 708  IARKLVALFHSRFDPAR-------RSQNDPGLAAEIERALDGVKNLDEDRILRRFLNLLC 760
            IAR LV+LF +RFDPA        R      L  +I  ALD V NLDEDRILR+FL +L 
Sbjct: 718  IARLLVSLFQARFDPAMGETHAAAREARVQDLQQQIAAALDDVPNLDEDRILRQFLGVLE 777

Query: 761  NTLRTNAYQNGADGRPKTYLSFKIDSRNIDDLPLPRPMVEVFVYSPRMEGVHLRGGKVAR 820
             TLRTN +Q  A   PK YLS K D   +  LP P+PM E++VYSPR+EGVHLRGGKVAR
Sbjct: 778  ATLRTNDFQRAAQHAPKPYLSLKFDPARVPGLPEPKPMFEIWVYSPRVEGVHLRGGKVAR 837

Query: 821  GGIRWSDRREDFRTEILGLMKAQMVKNTVIVPVGSKGGFVVKRPPPPSAGREAQLAEGIE 880
            GG+RWSDRREDFRTE+LGL+KAQMVKNTVIVPVGSKGGFVVK+ P   A REA L EG+ 
Sbjct: 838  GGLRWSDRREDFRTEVLGLVKAQMVKNTVIVPVGSKGGFVVKQAP---AEREAYLKEGVA 894

Query: 881  CYKTLMRGLLDITDNLDAQGAVVPPPEVVRHDGDDPYLVVAADKGTATFSDIANSVSVDH 940
            CY+T +RGLLD+TDNL  +G +VPPP+VVR D DDPYLVVAADKGTATFSD AN++S ++
Sbjct: 895  CYQTFLRGLLDLTDNL-VEGRLVPPPDVVRFDPDDPYLVVAADKGTATFSDYANAISAEY 953

Query: 941  GFWLGDAFASGGSAGYDHKKMGITARGAWESVKRHFRELGHDTQTQDFTVVGVGDMSGDV 1000
            GFWL DAFASGGS GYDHKKMGITARGAWESVKRHFRE+G DTQ  DFTV G+GDMSGDV
Sbjct: 954  GFWLDDAFASGGSVGYDHKKMGITARGAWESVKRHFREMGVDTQQTDFTVAGIGDMSGDV 1013

Query: 1001 FGNGMLLSKHIRLLAAFDHRHIFIDPDPDAARSWEERQRLFDLPRSSWADYDASLLSAGG 1060
            FGN MLLS+HIRL+AAFDHRHIF+DP PD   S+ ER+RLF LPRSSW DYD + +S GG
Sbjct: 1014 FGNAMLLSRHIRLVAAFDHRHIFLDPAPDPQVSFAERERLFKLPRSSWDDYDRAAISPGG 1073

Query: 1061 RVFDRSAKSLELTPEIRQRFGIAKDHVTPLELMQTLLKAEVDLLWFGGIGTYLKAAEETN 1120
             VF R+ KS+ L+P++R   G+++  + P +LM+ +L+A VDL + GGIGTY+KA+ E++
Sbjct: 1074 GVFARTVKSIVLSPQVRAALGVSEAELAPADLMRAILRAPVDLFYNGGIGTYVKASYESH 1133

Query: 1121 AEVGDKANDALRIDGRDVRAKVIGEGANLGVTQRGRIEAAQHGVRLNTDAIDNSAGVDTS 1180
            A+VGD+ANDA+R+DG D+R KV+ EG NLG TQ GRIE AQ G R+NTDAIDNSAGVD S
Sbjct: 1134 AQVGDRANDAVRVDGADLRCKVVAEGGNLGCTQFGRIEFAQRGGRINTDAIDNSAGVDCS 1193

Query: 1181 DHEVNIKILLNDVVVRGDMTLKQRDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDA 1240
            DHEVNIKILL  VV  G+MTLKQR+ LLA+M DEV  LVL DNY Q++AL++AR + P  
Sbjct: 1194 DHEVNIKILLGLVVADGEMTLKQRNALLASMADEVGELVLRDNYYQTRALSLARDRAPAW 1253

Query: 1241 LEAQARLIRSLEKAGRLNRAIEYLPDEEELSARMANREGLTRPELAVLLAYAKITLYDDL 1300
            L+A+ARL+  LE+ GRLNRAIE+LPD+ E+  R A  +GLT PE AVL+AY+K+ L D L
Sbjct: 1254 LDAEARLMAMLEREGRLNRAIEFLPDDAEIERRRAGGQGLTSPERAVLMAYSKMWLSDLL 1313

Query: 1301 LASDLPDDPFMADDLTRYFPKPLRKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKE 1360
            LASDL + PF+A DL  YFP+PLR   A+A+ RH L+REI+AT + N+LVNR G TFV  
Sbjct: 1314 LASDLLEAPFVARDLPLYFPQPLRSRFAQAMTRHPLQREILATMLANALVNRAGVTFVHR 1373

Query: 1361 MMEKTGMGPADVARAYTIVRDAFGLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAA 1420
            M E+TG  PA V RA  I R  F L  +W  I+ LD  V    Q +M  +T   +ERA  
Sbjct: 1374 MTEETGAEPAQVVRASLIARAVFRLDDVWQAIDALDDRVGHEAQAAMFADTSLLLERATL 1433

Query: 1421 WFLASCQQPLDIARETEAFRPGIETLLAGLDNVLDAEETARLTARVASYQEQGVPAELAR 1480
            WFL         +R  E F   +  L   LD +L  +E   L  R ++  E GVP  LA 
Sbjct: 1434 WFLHHQAGGAQASRAIEDFGAAVADLAPALDGLLVEDEAQALAQRQSALVEGGVPDALAL 1493

Query: 1481 RMAALPVLAAAPDLVRIAGRTGRGVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQ 1540
            ++A+   L A  D+  +A   GR +   A+VYF L +  G  WL D  A+  A  HWQ  
Sbjct: 1494 QLASTEALVATLDIAEVAAACGRSLRVSASVYFALDQLLGYAWLHDGIASLPARTHWQML 1553

Query: 1541 AVAALVDDLFAHQTALTTRVLEAVDQ-LPAEAPVEAWIAHRRPVVERVEQLLSELRTQPN 1599
            A AAL + L   +  LT  VL    Q   A   +EAW + R   + R  +L ++      
Sbjct: 1554 ARAALFETLAQVKRGLTRSVLRLSPQGDDALVLIEAWRSQREEPLARYRRLAADQHAAGP 1613

Query: 1600 VDLSMLAVANRQL 1612
             DL+ML+V  + L
Sbjct: 1614 ADLAMLSVTLKAL 1626


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: 5926
Number of extensions: 258
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: 1618
Length of database: 1639
Length adjustment: 52
Effective length of query: 1566
Effective length of database: 1587
Effective search space:  2485242
Effective search space used:  2485242
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 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