Alignments for a candidate for gdhA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Pseudomonas fluorescens GW456-L13

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate PfGW456L13_3298 NAD-specific glutamate dehydrogenase (EC 1.4.1.2), large form

Query= SwissProt::Q9HZE0
         (1620 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3298
          Length = 1632

 Score = 2718 bits (7046), Expect = 0.0
 Identities = 1344/1616 (83%), Positives = 1464/1616 (90%), Gaps = 2/1616 (0%)

Query: 1    MAFFTAASKADFQHQLQTALAQHLGDKALPQVTLFAEQFFSLISLDELTQRRLSDLVGCT 60
            MAFFTAASKADFQHQLQ ALAQH+ ++ALPQV LF+EQFF +ISLDELTQRRLSDL GCT
Sbjct: 1    MAFFTAASKADFQHQLQAALAQHISEQALPQVALFSEQFFGIISLDELTQRRLSDLAGCT 60

Query: 61   LSAWRLLERFDRDQPEVRVYNPDYEKHGWQSTHTAVEVLHPDLPFLVDSVRMELNRRGYS 120
            LSAWR+LERFD  QP+VRVYNPDYE+HGWQSTHTAVEVLH DLPFLVDSVR ELNRRGYS
Sbjct: 61   LSAWRMLERFDHAQPQVRVYNPDYERHGWQSTHTAVEVLHHDLPFLVDSVRTELNRRGYS 120

Query: 121  IHTLQTNVLSVRRSAKGELKEILPKGSQGKDVSQESLMYLEIDRCAHAGELRALEKAILE 180
            IHTLQT VLSVRR +KGEL EILPKG+QG D+ QESLMYLEIDRCA+  EL  L K + +
Sbjct: 121  IHTLQTTVLSVRRGSKGELLEILPKGTQGDDIQQESLMYLEIDRCANTAELNVLSKELEQ 180

Query: 181  VLGEVRVTVADFEPMKAKARELLTWLGKAKLKVPAEELKEVRSYLEWLLDNHFTFLGYEE 240
            VLGEVRV V DFEPMKAK +++LT L  ++  V  +E  E++S+LEWL+ NHFTFLGYEE
Sbjct: 181  VLGEVRVAVGDFEPMKAKVQDILTKLDNSQFAVDGDEKNEIKSFLEWLVGNHFTFLGYEE 240

Query: 241  FSVADEADGGRMVYDEKSFLGLTRLLRAGLSKDDLHIEDYAVAYLREPVLLSFAKAAHPS 300
            F V+DEADGG +VYD+ SFLGLT+LLRAGL+ DDL IEDYAV YLREP LLSFAKAAHPS
Sbjct: 241  FVVSDEADGGHIVYDKDSFLGLTKLLRAGLTYDDLRIEDYAVNYLREPTLLSFAKAAHPS 300

Query: 301  RVHRPAYPDYVSIRELDGKGRVIRECRFMGLFTSSVYNESVNDIPFIRGKVAEVMRRSGF 360
            RVHRPAYPDYVSIRE+D  G+VI+ECRFMGL+TSSVY ESV  IP+IR KV E+ RRSGF
Sbjct: 301  RVHRPAYPDYVSIREIDADGKVIKECRFMGLYTSSVYGESVRVIPYIRRKVEEIERRSGF 360

Query: 361  DTKAHLGKELAQVLEVLPRDDLFQTPVDELFSTALAIVRIQERNKIRVFLRKDPYGRFCY 420
              KAHLGKELAQVLEVLPRDDLFQTPVDELFST ++IV+IQERNKIRVFLRKDPYGRFCY
Sbjct: 361  QAKAHLGKELAQVLEVLPRDDLFQTPVDELFSTVMSIVQIQERNKIRVFLRKDPYGRFCY 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+QACRSWQDDY++L VE+ GEA GTNVLADFPKGFPAGYRERFA H AVVD+
Sbjct: 481  PLLLEKEVVQACRSWQDDYAALTVESFGEAHGTNVLADFPKGFPAGYRERFAAHSAVVDM 540

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

Query: 599  PYRLRHQNGREYWIHDFAFTYAEGLDVDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTA 658
            PYRLRH +GRE+WIHDFAFT AEGL++DIQQLN+ LQDAFVHIV GDAEND FNRLVLTA
Sbjct: 601  PYRLRHNSGREFWIHDFAFTAAEGLELDIQQLNDTLQDAFVHIVRGDAENDGFNRLVLTA 660

Query: 659  NLPWRDVALLRAYARYLKQIRLGFDLGYIASALNAHTDIARELVRLFKTRFYLARKLTAE 718
             LPWRDVALLRAYARY+KQIRLGFDLGYIAS LN HTDIA EL RLFKTRFYLARKLT E
Sbjct: 661  GLPWRDVALLRAYARYMKQIRLGFDLGYIASTLNNHTDIAHELTRLFKTRFYLARKLTGE 720

Query: 719  DLEDKQQKLEQAILGALDEVQVLNEDRILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFK 778
            DL DKQQ+LE AIL ALD+VQVLNEDRILRRYLDLIKATLRTNFYQ D NG NKSYFSFK
Sbjct: 721  DLGDKQQRLEHAILSALDDVQVLNEDRILRRYLDLIKATLRTNFYQTDANGHNKSYFSFK 780

Query: 779  FNPKAIPELPRPVPKYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQ 838
            FNP  IPELP+PVPK+EIFVYSPRVEGVHLR G VARGGLRWSDREEDFRTEVLGLVKAQ
Sbjct: 781  FNPHLIPELPKPVPKFEIFVYSPRVEGVHLRFGNVARGGLRWSDREEDFRTEVLGLVKAQ 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+ ASSF ERQRLF+LPRS+W+DYD  L+S GGGIF RSAKSIAI+P+M+ RFDIQAD
Sbjct: 1021 PNPEPASSFAERQRLFDLPRSAWSDYDTSLMSEGGGIFSRSAKSIAISPQMQERFDIQAD 1080

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

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

Query: 1199 ALLVKMTDAVGALVLGNNYKQTQALSLAQRRARERIAEYKRLMGDLEARGKLDRALEFLP 1258
             LL  MTD VG LVLGNNYKQTQALSLA RRA  RIAEYKRLM DLE RGKLDRA+EFLP
Sbjct: 1201 ELLASMTDEVGGLVLGNNYKQTQALSLAARRALPRIAEYKRLMNDLEGRGKLDRAIEFLP 1260

Query: 1259 SDEELAERISAGQGLTRAELSVLISYSKIDLKESLLKSLVPDDDYLTRDMETAFPALLAE 1318
            ++E + ERI+ G GLTRAELSVLISYSKIDLKE LL SLVPDDDYLTRDMETAFP  L  
Sbjct: 1261 AEEAINERIAEGHGLTRAELSVLISYSKIDLKEQLLGSLVPDDDYLTRDMETAFPPTLVS 1320

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

Query: 1379 PHWFRQIENLDYQVPADIQLTLMDELMRLGRRATRWFLRSRRNELDAARDVAHFGPRIAA 1438
            PHWFRQIENLDY+V AD+QL LMDELMRLGRRATRWFLR+RRNE +AARDVAHFGP +AA
Sbjct: 1381 PHWFRQIENLDYKVSADVQLELMDELMRLGRRATRWFLRARRNEQNAARDVAHFGPHLAA 1440

Query: 1439 LGLKLNELLEGPTRELWQARYQTYVDAGVPELLARMVAGTSHLYTLLPIIEASDVTGQDT 1498
            LGLKL+ELL G  RE WQ RYQ YV+AGVPELLARMVAGT+HLYTLLPIIEASDVTGQD 
Sbjct: 1441 LGLKLDELLSGEIRETWQTRYQAYVEAGVPELLARMVAGTTHLYTLLPIIEASDVTGQDP 1500

Query: 1499 AEVAKAYFAVGSALDLTWYLQQITNLPVENNWQALAREAFRDDLDWQQRAITVSVLQMQD 1558
            A+VAKAYFAVGSALD+TWYLQQI+ LPVENNWQALAREAFRDD+DWQQRAIT+SVLQ  D
Sbjct: 1501 ADVAKAYFAVGSALDITWYLQQISALPVENNWQALAREAFRDDVDWQQRAITISVLQQGD 1560

Query: 1559 GPKEVEARVGLWLEQHLPLVERWRAMLVELRAASGTDYAMYAVANRELMDLAQSSQ 1614
            G +EVE R+ LW++QH  ++ERWRAMLVE+RAASGTDYAMYAVANREL+DLA S Q
Sbjct: 1561 GSQEVETRLDLWMQQHESMIERWRAMLVEIRAASGTDYAMYAVANRELLDLALSGQ 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: 6681
Number of extensions: 250
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: 1632
Length adjustment: 52
Effective length of query: 1568
Effective length of database: 1580
Effective search space:  2477440
Effective search space used:  2477440
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