GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Pseudomonas simiae WCS417

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate GFF2946 PS417_15075 NAD-glutamate dehydrogenase

Query= SwissProt::Q9HZE0
         (1620 letters)



>FitnessBrowser__WCS417:GFF2946
          Length = 1622

 Score = 2712 bits (7031), Expect = 0.0
 Identities = 1343/1616 (83%), Positives = 1466/1616 (90%), Gaps = 2/1616 (0%)

Query: 1    MAFFTAASKADFQHQLQTALAQHLGDKALPQVTLFAEQFFSLISLDELTQRRLSDLVGCT 60
            MAFFTAASKADFQHQLQ ALAQH+ ++ALPQV LFAEQFF +ISLDELTQRRLSDL GCT
Sbjct: 1    MAFFTAASKADFQHQLQAALAQHISEQALPQVALFAEQFFGIISLDELTQRRLSDLAGCT 60

Query: 61   LSAWRLLERFDRDQPEVRVYNPDYEKHGWQSTHTAVEVLHPDLPFLVDSVRMELNRRGYS 120
            LSAWRLLERFD  QP+VRVYNPDYE+HGWQSTHTAVEVLH DLPFLVDSVR ELNRRGYS
Sbjct: 61   LSAWRLLERFDHTQPQVRVYNPDYERHGWQSTHTAVEVLHHDLPFLVDSVRTELNRRGYS 120

Query: 121  IHTLQTNVLSVRRSAKGELKEILPKGSQGKDVSQESLMYLEIDRCAHAGELRALEKAILE 180
            IHTLQT VLSVRR AKGEL EILPKG+QG+ + QESLMYLEIDRCA+A EL  L K + +
Sbjct: 121  IHTLQTTVLSVRRGAKGELLEILPKGTQGEGIQQESLMYLEIDRCANAAELNVLSKELEQ 180

Query: 181  VLGEVRVTVADFEPMKAKARELLTWLGKAKLKVPAEELKEVRSYLEWLLDNHFTFLGYEE 240
            VLGEVRV VADFEPMKAK ++LL  +  ++  +  EE  E++++LEWL+ NHFTFLGYEE
Sbjct: 181  VLGEVRVAVADFEPMKAKVQDLLAGIDASQFSIDGEEKAEIKNFLEWLVGNHFTFLGYEE 240

Query: 241  FSVADEADGGRMVYDEKSFLGLTRLLRAGLSKDDLHIEDYAVAYLREPVLLSFAKAAHPS 300
            F V DEADGG + YD  SFLGLT+LLRAGL+ DDL IEDYAVAYLREP +LSFAKAAHPS
Sbjct: 241  FVVRDEADGGHIEYDADSFLGLTKLLRAGLTADDLRIEDYAVAYLREPTVLSFAKAAHPS 300

Query: 301  RVHRPAYPDYVSIRELDGKGRVIRECRFMGLFTSSVYNESVNDIPFIRGKVAEVMRRSGF 360
            RVHRPAYPDYVSIRE+   G+VI+E RFMGL+TSSVY ESV  IP+IR KVAE+ RRSGF
Sbjct: 301  RVHRPAYPDYVSIREISADGKVIKEHRFMGLYTSSVYGESVRVIPYIRRKVAEIERRSGF 360

Query: 361  DTKAHLGKELAQVLEVLPRDDLFQTPVDELFSTALAIVRIQERNKIRVFLRKDPYGRFCY 420
              KAHLGKELAQV+EVLPRDDLFQTPVDELFST ++IV+IQERNKIRVFLRKDPYGRFCY
Sbjct: 361  QPKAHLGKELAQVVEVLPRDDLFQTPVDELFSTVMSIVQIQERNKIRVFLRKDPYGRFCY 420

Query: 421  CLAYVPRDVYSTETRLKIQQVLMERLQASDCEFWTFFSESVLARVQFILRVDPKSRIDID 480
            CLAYVPRD+YSTE R KIQQVLM+RL+ASDCEFWTFFSESVLARVQ ILRVDPK+R+DID
Sbjct: 421  CLAYVPRDIYSTEVRQKIQQVLMDRLKASDCEFWTFFSESVLARVQLILRVDPKNRLDID 480

Query: 481  PARLEEEVIQACRSWQDDYSSLVVENLGEAKGTNVLADFPKGFPAGYRERFAPHFAVVDL 540
            P +LE+EV+QACRSWQDDYSSLVVE+ GEA GTNVLADFPKGFPAGYRERFA H AVVD+
Sbjct: 481  PLQLEKEVVQACRSWQDDYSSLVVESFGEAHGTNVLADFPKGFPAGYRERFAAHSAVVDM 540

Query: 541  QHLLSLSEQRPLVMSFYQPLAQ--GEQQLHCKLYHADTPLALSDVLPILENLGLRVLGEF 598
            QHLLSL+E  PLVMSFYQPL Q  G+++LHCKLYHADTPLALSDVLPILENLGLRVLGEF
Sbjct: 541  QHLLSLTEANPLVMSFYQPLGQVSGQRELHCKLYHADTPLALSDVLPILENLGLRVLGEF 600

Query: 599  PYRLRHQNGREYWIHDFAFTYAEGLDVDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTA 658
            PYRLRH NGRE+WIHDFAF  AEG+++DIQQLN+ LQDAFVHIV GDAENDAFNRLVLTA
Sbjct: 601  PYRLRHANGREFWIHDFAFIAAEGVNLDIQQLNDTLQDAFVHIVHGDAENDAFNRLVLTA 660

Query: 659  NLPWRDVALLRAYARYLKQIRLGFDLGYIASALNAHTDIARELVRLFKTRFYLARKLTAE 718
             LPWRDVALLRAYARYLKQIRLGFDLGYIAS LN HTDIAREL RLFKTRFYLARKLTA+
Sbjct: 661  GLPWRDVALLRAYARYLKQIRLGFDLGYIASTLNNHTDIARELTRLFKTRFYLARKLTAD 720

Query: 719  DLEDKQQKLEQAILGALDEVQVLNEDRILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFK 778
            DLEDKQQ+LEQAIL ALD+VQVLNEDRILRRYLDLIKATLRTNFYQ D NGQNKSYFSFK
Sbjct: 721  DLEDKQQRLEQAILSALDDVQVLNEDRILRRYLDLIKATLRTNFYQTDANGQNKSYFSFK 780

Query: 779  FNPKAIPELPRPVPKYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQ 838
            F+P+AIPELP+PVPK+EIFVYSPRVEGVHLR G VARGGLRWSDREEDFRTEVLGLVKAQ
Sbjct: 781  FDPRAIPELPKPVPKFEIFVYSPRVEGVHLRFGNVARGGLRWSDREEDFRTEVLGLVKAQ 840

Query: 839  QVKNAVIVPVGAKGGFVPRRLPLGGSRDEIQAEAIACYRIFISGLLDITDNLKEGEVVPP 898
            QVKN+VIVPVGAKGGF+PRRLPLGGSRDEI AE IACYRIFISGLLDITDNLK+G +VPP
Sbjct: 841  QVKNSVIVPVGAKGGFLPRRLPLGGSRDEIAAEGIACYRIFISGLLDITDNLKDGALVPP 900

Query: 899  ANVVRHDEDDPYLVVAADKGTATFSDIANGIAAEYGFWLGDAFASGGSAGYDHKGMGITA 958
            ANVVRHD+DDPYLVVAADKGTATFSDIANGIA +YGFWLGDAFASGGSAGYDHK MGITA
Sbjct: 901  ANVVRHDDDDPYLVVAADKGTATFSDIANGIAIDYGFWLGDAFASGGSAGYDHKKMGITA 960

Query: 959  KGAWVSVQRHFRERGIDVQKDNISVIGIGDMAGDVFGNGLLMSDKLQLVAAFNHMHIFID 1018
            KGAWV VQRHFRERGI+VQ+D+I+V+G+GDMAGDVFGNGLLMSDKLQLVAAFNH+HIFID
Sbjct: 961  KGAWVGVQRHFRERGINVQEDSITVVGVGDMAGDVFGNGLLMSDKLQLVAAFNHLHIFID 1020

Query: 1019 PNPDAASSFVERQRLFNLPRSSWADYDAKLISAGGGIFLRSAKSIAITPEMKARFDIQAD 1078
            PNP+ A+SFVERQR+F LPRS+W DYD  ++S GGGIF RSAKSIAI+P+MK RFDI AD
Sbjct: 1021 PNPNPATSFVERQRMFELPRSAWTDYDTSIMSEGGGIFSRSAKSIAISPQMKERFDISAD 1080

Query: 1079 RLAPTELIHALLKAPVDLLWNGGIGTYVKSSKETHADVGDKANDGLRVDGRELRAKVVGE 1138
            +L PTEL++ALLKAPVDLLWNGGIGTYVK+S E+HADVGDKAND LRV+G ELR KVVGE
Sbjct: 1081 KLTPTELLNALLKAPVDLLWNGGIGTYVKASTESHADVGDKANDALRVNGNELRCKVVGE 1140

Query: 1139 GGNLGMTQLARVEFGLHGGANNTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMTEKQRN 1198
            GGNLGMTQL RVEFGL+GG +NTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMT+KQRN
Sbjct: 1141 GGNLGMTQLGRVEFGLNGGGSNTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMTDKQRN 1200

Query: 1199 ALLVKMTDAVGALVLGNNYKQTQALSLAQRRARERIAEYKRLMGDLEARGKLDRALEFLP 1258
             LL  MTD VG LVLGNNYKQTQALSLA RRA ER AEYKRLM DLE RGKLDRA+E+LP
Sbjct: 1201 QLLASMTDEVGNLVLGNNYKQTQALSLAARRAYERAAEYKRLMSDLEGRGKLDRAIEYLP 1260

Query: 1259 SDEELAERISAGQGLTRAELSVLISYSKIDLKESLLKSLVPDDDYLTRDMETAFPALLAE 1318
            ++E+L ER + G+GLTR ELSVLISYSKIDLKE+LLKSLVPDD+YLTRDMETAFP  L  
Sbjct: 1261 TEEQLTERAATGKGLTRPELSVLISYSKIDLKEALLKSLVPDDEYLTRDMETAFPPSLVA 1320

Query: 1319 KFGDAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSAANVAGAYVIVRDVFHL 1378
            KF +AMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMS ANVAGAYVIVRD+FHL
Sbjct: 1321 KFSEAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSPANVAGAYVIVRDIFHL 1380

Query: 1379 PHWFRQIENLDYQVPADIQLTLMDELMRLGRRATRWFLRSRRNELDAARDVAHFGPRIAA 1438
            PHWFRQIE LD+QV AD+QL LMDELMRLGRRATRWFLRSRRNE DA RD AHFGP +AA
Sbjct: 1381 PHWFRQIEALDHQVSADVQLELMDELMRLGRRATRWFLRSRRNEQDAGRDTAHFGPHLAA 1440

Query: 1439 LGLKLNELLEGPTRELWQARYQTYVDAGVPELLARMVAGTSHLYTLLPIIEASDVTGQDT 1498
            LGLKL+ELLEGPTRE WQ RY  Y +AGVPELLARMVAGT+HLYTLLPIIEA+DVTG D 
Sbjct: 1441 LGLKLDELLEGPTREGWQNRYGKYTEAGVPELLARMVAGTTHLYTLLPIIEAADVTGHDA 1500

Query: 1499 AEVAKAYFAVGSALDLTWYLQQITNLPVENNWQALAREAFRDDLDWQQRAITVSVLQMQD 1558
            AEVAKAYFAVGSALDL WYLQQI++LPV NNWQA AREAFRDD+DWQQRAIT+SVLQM D
Sbjct: 1501 AEVAKAYFAVGSALDLPWYLQQISDLPVANNWQAQAREAFRDDVDWQQRAITISVLQMAD 1560

Query: 1559 GPKEVEARVGLWLEQHLPLVERWRAMLVELRAASGTDYAMYAVANRELMDLAQSSQ 1614
             P+++EARV LWLEQH  + +RW AM+VE+RAA GTDYAMYAVANREL+DLA S Q
Sbjct: 1561 APQDMEARVALWLEQHKDMADRWVAMMVEIRAAVGTDYAMYAVANRELLDLALSGQ 1616


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: 6529
Number of extensions: 251
Number of successful extensions: 3
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: 1622
Length adjustment: 51
Effective length of query: 1569
Effective length of database: 1571
Effective search space:  2464899
Effective search space used:  2464899
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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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:

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:

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:

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:

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