Alignments for a candidate for gdhA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Pseudomonas putida KT2440

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate PP_2080 PP_2080 NAD-specific glutamate dehydrogenase

Query= SwissProt::Q9HZE0
         (1620 letters)



>FitnessBrowser__Putida:PP_2080
          Length = 1621

 Score = 2719 bits (7047), Expect = 0.0
 Identities = 1353/1618 (83%), Positives = 1472/1618 (90%), Gaps = 1/1618 (0%)

Query: 1    MAFFTAASKADFQHQLQTALAQHLGDKALPQVTLFAEQFFSLISLDELTQRRLSDLVGCT 60
            MAFFTAASKADFQHQLQ ALAQH+ +++LPQV LFAEQFF +ISLDELTQRRLSDL GCT
Sbjct: 1    MAFFTAASKADFQHQLQAALAQHISEQSLPQVALFAEQFFGIISLDELTQRRLSDLAGCT 60

Query: 61   LSAWRLLERFDRDQPEVRVYNPDYEKHGWQSTHTAVEVLHPDLPFLVDSVRMELNRRGYS 120
            LSAWR++ERFD + P+VRVYNPDYE++GWQSTHT VEVLH DLPFLVDSVR ELNRRGYS
Sbjct: 61   LSAWRIIERFDPEYPQVRVYNPDYERNGWQSTHTVVEVLHHDLPFLVDSVRTELNRRGYS 120

Query: 121  IHTLQTNVLSVRRSAKGELKEILPKGSQGKDVSQESLMYLEIDRCAHAGELRALEKAILE 180
            IHTLQT VLSVRR AKGEL E+LPKG+QG+ V  ESLMYLEIDRCA+A EL  L + I +
Sbjct: 121  IHTLQTTVLSVRRGAKGELLELLPKGTQGEGVRYESLMYLEIDRCANAAELTVLTREIEQ 180

Query: 181  VLGEVRVTVADFEPMKAKARELLTWLGKAKLKVPAEELKEVRSYLEWLLDNHFTFLGYEE 240
            VL EVRV VADFEPMKAK RE++  + +        E  EV+++LEWLLDNHFTFLGYEE
Sbjct: 181  VLAEVRVVVADFEPMKAKLREVVAQVEQTAFGPAQNEKGEVKAFLEWLLDNHFTFLGYEE 240

Query: 241  FSVADEADGGRMVYDEKSFLGLTRLLRAGLSKDDLHIEDYAVAYLREPVLLSFAKAAHPS 300
            F+V  +ADGG+MVYDE+SFLGL R LR GL+ ++L IEDYAVAYL EP+LLSFAKAA PS
Sbjct: 241  FTVKGDADGGQMVYDEQSFLGLPRRLRVGLTAEELRIEDYAVAYLNEPLLLSFAKAALPS 300

Query: 301  RVHRPAYPDYVSIRELDGKGRVIRECRFMGLFTSSVYNESVNDIPFIRGKVAEVMRRSGF 360
            RVHRPAYPDYVSIR+LD  G+VI+E RFMGL+TSSVY ESV+ IP+IR KVAEV RRSGF
Sbjct: 301  RVHRPAYPDYVSIRQLDADGKVIKEHRFMGLYTSSVYGESVHAIPYIRVKVAEVERRSGF 360

Query: 361  DTKAHLGKELAQVLEVLPRDDLFQTPVDELFSTALAIVRIQERNKIRVFLRKDPYGRFCY 420
            D KAHLGKELAQVLEVLPRDDLFQTP+DELFST +AIV+IQERNKIRVFLRKDPYGRFCY
Sbjct: 361  DPKAHLGKELAQVLEVLPRDDLFQTPIDELFSTVMAIVQIQERNKIRVFLRKDPYGRFCY 420

Query: 421  CLAYVPRDVYSTETRLKIQQVLMERLQASDCEFWTFFSESVLARVQFILRVDPKSRIDID 480
            CLAYVPR++YSTE R KIQQVLMERL+ASDCEFWTFFSESVLARVQ ILRVDPK+RIDID
Sbjct: 421  CLAYVPREIYSTEVRQKIQQVLMERLKASDCEFWTFFSESVLARVQLILRVDPKNRIDID 480

Query: 481  PARLEEEVIQACRSWQDDYSSLVVENLGEAKGTNVLADFPKGFPAGYRERFAPHFAVVDL 540
            P +LE EVIQACRSW DDYS+LVVEN GEA+GTN+LADFPKGFPAGYRERFA H AVVDL
Sbjct: 481  PQQLEREVIQACRSWHDDYSALVVENFGEAQGTNILADFPKGFPAGYRERFAAHSAVVDL 540

Query: 541  QHLLSLSEQRPLVMSFYQPLAQ-GEQQLHCKLYHADTPLALSDVLPILENLGLRVLGEFP 599
            QH+L+LSE +PL MSFYQPL Q GE+ LHCKLYHADTPLALSDVLPILENLGLRVLGEFP
Sbjct: 541  QHVLNLSESKPLAMSFYQPLTQVGERILHCKLYHADTPLALSDVLPILENLGLRVLGEFP 600

Query: 600  YRLRHQNGREYWIHDFAFTYAEGLDVDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTAN 659
            YRLRH NGREYWIHDFAFTY+EGL +DIQQLN+ LQDAF+HIV GDAENDAFNRLVLTA 
Sbjct: 601  YRLRHANGREYWIHDFAFTYSEGLSLDIQQLNDTLQDAFIHIVRGDAENDAFNRLVLTAG 660

Query: 660  LPWRDVALLRAYARYLKQIRLGFDLGYIASALNAHTDIARELVRLFKTRFYLARKLTAED 719
            LPWRDVALLRAYARYLKQIRLGFDLGYIAS LN HTDIAREL RLFKTRFYLARKLT +D
Sbjct: 661  LPWRDVALLRAYARYLKQIRLGFDLGYIASTLNNHTDIARELTRLFKTRFYLARKLTQDD 720

Query: 720  LEDKQQKLEQAILGALDEVQVLNEDRILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFKF 779
            L+DKQQ+LEQAIL ALD+VQVLNEDRILRRYLDLIKATLRTNFYQPD NGQNKSYFSFKF
Sbjct: 721  LDDKQQRLEQAILSALDDVQVLNEDRILRRYLDLIKATLRTNFYQPDANGQNKSYFSFKF 780

Query: 780  NPKAIPELPRPVPKYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQQ 839
            NPK IPELP+PVPK+EIFVYSPRVEGVHLR G VARGGLRWSDREEDFRTEVLGLVKAQQ
Sbjct: 781  NPKLIPELPKPVPKFEIFVYSPRVEGVHLRFGNVARGGLRWSDREEDFRTEVLGLVKAQQ 840

Query: 840  VKNAVIVPVGAKGGFVPRRLPLGGSRDEIQAEAIACYRIFISGLLDITDNLKEGEVVPPA 899
            VKN+VIVPVGAKGGF+PRRLPLGGSRDEI AE +ACYRIFISGLLDITDNLK+G VVPPA
Sbjct: 841  VKNSVIVPVGAKGGFLPRRLPLGGSRDEIAAEGVACYRIFISGLLDITDNLKDGGVVPPA 900

Query: 900  NVVRHDEDDPYLVVAADKGTATFSDIANGIAAEYGFWLGDAFASGGSAGYDHKGMGITAK 959
            NVVRHD+DDPYLVVAADKGTATFSDIANGIA +YGFWLGDAFASGGSAGYDHK MGITA+
Sbjct: 901  NVVRHDDDDPYLVVAADKGTATFSDIANGIAIDYGFWLGDAFASGGSAGYDHKKMGITAR 960

Query: 960  GAWVSVQRHFRERGIDVQKDNISVIGIGDMAGDVFGNGLLMSDKLQLVAAFNHMHIFIDP 1019
            GAWV VQRHFRERGI+VQ+D I+VIG+GDMAGDVFGNGLLMSDKLQLVAAFNH+HIFIDP
Sbjct: 961  GAWVGVQRHFRERGINVQEDPITVIGVGDMAGDVFGNGLLMSDKLQLVAAFNHLHIFIDP 1020

Query: 1020 NPDAASSFVERQRLFNLPRSSWADYDAKLISAGGGIFLRSAKSIAITPEMKARFDIQADR 1079
            NPD A+SF ER+RLF+LPRS+W+DYD  ++S GGGIF RSAKSIAI+P+MK RF I+ADR
Sbjct: 1021 NPDPATSFAERKRLFDLPRSAWSDYDTSIMSEGGGIFPRSAKSIAISPQMKERFAIEADR 1080

Query: 1080 LAPTELIHALLKAPVDLLWNGGIGTYVKSSKETHADVGDKANDGLRVDGRELRAKVVGEG 1139
            L PTEL++ALLKAPVDLLWNGGIGTYVK+S E+HADVGDKAND LRV+G ELR KVVGEG
Sbjct: 1081 LTPTELLNALLKAPVDLLWNGGIGTYVKASTESHADVGDKANDALRVNGNELRCKVVGEG 1140

Query: 1140 GNLGMTQLARVEFGLHGGANNTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMTEKQRNA 1199
            GNLGMTQL RVEFGL+GGA NTDFIDNAGGVDCSDHEVNIKILLNEVVQ GDMTEKQRN 
Sbjct: 1141 GNLGMTQLGRVEFGLNGGATNTDFIDNAGGVDCSDHEVNIKILLNEVVQGGDMTEKQRNQ 1200

Query: 1200 LLVKMTDAVGALVLGNNYKQTQALSLAQRRARERIAEYKRLMGDLEARGKLDRALEFLPS 1259
            LL  MTD V  LVLGNNYKQTQALSLA RRARERIAEYKRLM DLEARGKLDRA+EFLPS
Sbjct: 1201 LLGSMTDEVAGLVLGNNYKQTQALSLAARRARERIAEYKRLMADLEARGKLDRAIEFLPS 1260

Query: 1260 DEELAERISAGQGLTRAELSVLISYSKIDLKESLLKSLVPDDDYLTRDMETAFPALLAEK 1319
            +E+LAER++AGQGLTRAELSVLISYSKIDLKE LLKSLVPDDDYLTRDMETAFP  L  K
Sbjct: 1261 EEQLAERLAAGQGLTRAELSVLISYSKIDLKEQLLKSLVPDDDYLTRDMETAFPPSLVSK 1320

Query: 1320 FGDAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSAANVAGAYVIVRDVFHLP 1379
            F +AMRRHRLKREIVSTQIANDLVN+MGITFVQRLKESTGMS ANVAGAYVIVRD+FHLP
Sbjct: 1321 FAEAMRRHRLKREIVSTQIANDLVNNMGITFVQRLKESTGMSPANVAGAYVIVRDIFHLP 1380

Query: 1380 HWFRQIENLDYQVPADIQLTLMDELMRLGRRATRWFLRSRRNELDAARDVAHFGPRIAAL 1439
            HWFRQIE LDYQVPA+IQLTLMDELMRLGRRATRWFLRSRRNE DA RD AHFGP+IA L
Sbjct: 1381 HWFRQIEALDYQVPAEIQLTLMDELMRLGRRATRWFLRSRRNEQDAGRDTAHFGPKIAQL 1440

Query: 1440 GLKLNELLEGPTRELWQARYQTYVDAGVPELLARMVAGTSHLYTLLPIIEASDVTGQDTA 1499
            GLKL+ELLEGPTRE W  RYQ +VDAGVPELLARMVAGTSHLYTLLPIIEA+DVTG + A
Sbjct: 1441 GLKLDELLEGPTRERWMVRYQGFVDAGVPELLARMVAGTSHLYTLLPIIEAADVTGHEPA 1500

Query: 1500 EVAKAYFAVGSALDLTWYLQQITNLPVENNWQALAREAFRDDLDWQQRAITVSVLQMQDG 1559
            +VAKA+FAVGSALDLTWYLQ+I+NLPVENNWQALAREAFRDD+D QQRAIT+SVLQM D 
Sbjct: 1501 QVAKAFFAVGSALDLTWYLQEISNLPVENNWQALAREAFRDDIDLQQRAITISVLQMADA 1560

Query: 1560 PKEVEARVGLWLEQHLPLVERWRAMLVELRAASGTDYAMYAVANRELMDLAQSSQHGV 1617
            P++++ARV LW EQH  +VERWRAML +LR A+GTDYAMYAVANREL+DLA S Q  V
Sbjct: 1561 PQDMDARVALWSEQHRGMVERWRAMLDDLRNATGTDYAMYAVANRELVDLAMSGQAAV 1618


Lambda     K      H
   0.321    0.137    0.403 

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: 6651
Number of extensions: 277
Number of successful extensions: 4
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: 1620
Length of database: 1621
Length adjustment: 51
Effective length of query: 1569
Effective length of database: 1570
Effective search space:  2463330
Effective search space used:  2463330
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 (21.9 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