Alignments for a candidate for gdhA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Azospirillum brasilense Sp245

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate AZOBR_RS00190 AZOBR_RS00190 NAD-glutamate dehydrogenase

Query= uniprot:G8AE86
         (1618 letters)



>FitnessBrowser__azobra:AZOBR_RS00190
          Length = 1618

 Score = 3192 bits (8277), Expect = 0.0
 Identities = 1618/1618 (100%), Positives = 1618/1618 (100%)

Query: 1    MALRAEQLKDELTEEVVRQVRERLGRSRAAPAERFVRQFYDNVPPDDIIQAPAEQLYGAA 60
            MALRAEQLKDELTEEVVRQVRERLGRSRAAPAERFVRQFYDNVPPDDIIQAPAEQLYGAA
Sbjct: 1    MALRAEQLKDELTEEVVRQVRERLGRSRAAPAERFVRQFYDNVPPDDIIQAPAEQLYGAA 60

Query: 61   LAMWQWGQQREATDRAKVRVYNPRVEEHGWQSHRTVVEIVNDDMPFLVDSVTAELNRQGL 120
            LAMWQWGQQREATDRAKVRVYNPRVEEHGWQSHRTVVEIVNDDMPFLVDSVTAELNRQGL
Sbjct: 61   LAMWQWGQQREATDRAKVRVYNPRVEEHGWQSHRTVVEIVNDDMPFLVDSVTAELNRQGL 120

Query: 121  TVHLVIHPVVRVKRDADGQLAELYEPAAAPTDAAPESFMHVEVGAVTGAAALDQAREGLE 180
            TVHLVIHPVVRVKRDADGQLAELYEPAAAPTDAAPESFMHVEVGAVTGAAALDQAREGLE
Sbjct: 121  TVHLVIHPVVRVKRDADGQLAELYEPAAAPTDAAPESFMHVEVGAVTGAAALDQAREGLE 180

Query: 181  RVLADVRAAVADWRAMRQQVRAAIVEADCARAAVPAIIPDDEVDEAKAFLSWADDDHFTF 240
            RVLADVRAAVADWRAMRQQVRAAIVEADCARAAVPAIIPDDEVDEAKAFLSWADDDHFTF
Sbjct: 181  RVLADVRAAVADWRAMRQQVRAAIVEADCARAAVPAIIPDDEVDEAKAFLSWADDDHFTF 240

Query: 241  LGYREYRFESGADGADSSLGLVAGSGLGILRDDSVTVFDGLRNYATLPPDVRDFLRNPRV 300
            LGYREYRFESGADGADSSLGLVAGSGLGILRDDSVTVFDGLRNYATLPPDVRDFLRNPRV
Sbjct: 241  LGYREYRFESGADGADSSLGLVAGSGLGILRDDSVTVFDGLRNYATLPPDVRDFLRNPRV 300

Query: 301  LMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPREIPYLRRK 360
            LMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPREIPYLRRK
Sbjct: 301  LMVTKGNRPSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPREIPYLRRK 360

Query: 361  VAEVMELAGFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQERQRLALFV 420
            VAEVMELAGFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQERQRLALFV
Sbjct: 361  VAEVMELAGFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQERQRLALFV 420

Query: 421  RKDPFERFASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVLARLHFIIR 480
            RKDPFERFASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVLARLHFIIR
Sbjct: 421  RKDPFERFASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVLARLHFIIR 480

Query: 481  TEPGRVPTVDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADAFPTAYREE 540
            TEPGRVPTVDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADAFPTAYREE
Sbjct: 481  TEPGRVPTVDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADAFPTAYREE 540

Query: 541  FNAEAAVFDIERIEKATAQGTLGINLYRPLEAEGDELHVKIYHEGRPVPLSDVLPMLEHM 600
            FNAEAAVFDIERIEKATAQGTLGINLYRPLEAEGDELHVKIYHEGRPVPLSDVLPMLEHM
Sbjct: 541  FNAEAAVFDIERIEKATAQGTLGINLYRPLEAEGDELHVKIYHEGRPVPLSDVLPMLEHM 600

Query: 601  DLKVITEAPFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQDAFAAVWDGRMEDD 660
            DLKVITEAPFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQDAFAAVWDGRMEDD
Sbjct: 601  DLKVITEAPFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQDAFAAVWDGRMEDD 660

Query: 661  GFNRLVLRAGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPAIARKLVALFHSRF 720
            GFNRLVLRAGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPAIARKLVALFHSRF
Sbjct: 661  GFNRLVLRAGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPAIARKLVALFHSRF 720

Query: 721  DPARRSQNDPGLAAEIERALDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYL 780
            DPARRSQNDPGLAAEIERALDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYL
Sbjct: 721  DPARRSQNDPGLAAEIERALDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYL 780

Query: 781  SFKIDSRNIDDLPLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLM 840
            SFKIDSRNIDDLPLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLM
Sbjct: 781  SFKIDSRNIDDLPLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLM 840

Query: 841  KAQMVKNTVIVPVGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQG 900
            KAQMVKNTVIVPVGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQG
Sbjct: 841  KAQMVKNTVIVPVGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQG 900

Query: 901  AVVPPPEVVRHDGDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKK 960
            AVVPPPEVVRHDGDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKK
Sbjct: 901  AVVPPPEVVRHDGDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKK 960

Query: 961  MGITARGAWESVKRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHR 1020
            MGITARGAWESVKRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHR
Sbjct: 961  MGITARGAWESVKRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHR 1020

Query: 1021 HIFIDPDPDAARSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRF 1080
            HIFIDPDPDAARSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRF
Sbjct: 1021 HIFIDPDPDAARSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRF 1080

Query: 1081 GIAKDHVTPLELMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRA 1140
            GIAKDHVTPLELMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRA
Sbjct: 1081 GIAKDHVTPLELMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRA 1140

Query: 1141 KVIGEGANLGVTQRGRIEAAQHGVRLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMT 1200
            KVIGEGANLGVTQRGRIEAAQHGVRLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMT
Sbjct: 1141 KVIGEGANLGVTQRGRIEAAQHGVRLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMT 1200

Query: 1201 LKQRDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRA 1260
            LKQRDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRA
Sbjct: 1201 LKQRDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRA 1260

Query: 1261 IEYLPDEEELSARMANREGLTRPELAVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFP 1320
            IEYLPDEEELSARMANREGLTRPELAVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFP
Sbjct: 1261 IEYLPDEEELSARMANREGLTRPELAVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFP 1320

Query: 1321 KPLRKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVR 1380
            KPLRKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVR
Sbjct: 1321 KPLRKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVR 1380

Query: 1381 DAFGLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQQPLDIARETEAFR 1440
            DAFGLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQQPLDIARETEAFR
Sbjct: 1381 DAFGLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQQPLDIARETEAFR 1440

Query: 1441 PGIETLLAGLDNVLDAEETARLTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGR 1500
            PGIETLLAGLDNVLDAEETARLTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGR
Sbjct: 1441 PGIETLLAGLDNVLDAEETARLTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGR 1500

Query: 1501 TGRGVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRV 1560
            TGRGVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRV
Sbjct: 1501 TGRGVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRV 1560

Query: 1561 LEAVDQLPAEAPVEAWIAHRRPVVERVEQLLSELRTQPNVDLSMLAVANRQLRGLTAG 1618
            LEAVDQLPAEAPVEAWIAHRRPVVERVEQLLSELRTQPNVDLSMLAVANRQLRGLTAG
Sbjct: 1561 LEAVDQLPAEAPVEAWIAHRRPVVERVEQLLSELRTQPNVDLSMLAVANRQLRGLTAG 1618


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: 7024
Number of extensions: 302
Number of successful extensions: 5
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: 1618
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1567
Effective search space:  2455489
Effective search space used:  2455489
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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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