Alignments for a candidate for gdhA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Marinobacter adhaerens HP15

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate GFF2321 HP15_2269 NAD-specific glutamate dehydrogenase

Query= SwissProt::Q9HZE0
         (1620 letters)



>FitnessBrowser__Marino:GFF2321
          Length = 1628

 Score = 1675 bits (4338), Expect = 0.0
 Identities = 842/1617 (52%), Positives = 1120/1617 (69%), Gaps = 2/1617 (0%)

Query: 1    MAFFTAASKADFQHQLQTALAQHLGDKALPQVTLFAEQFFSLISLDELTQRRLSDLVGCT 60
            M   T ASK  F  QL  A A+ +      +++ FA+Q ++ I L+EL  RR +D  G  
Sbjct: 1    MNALTVASKDQFFEQLADAFAKKISKTEAKKISEFAKQHYAHIPLEELVSRRFADTYGAV 60

Query: 61   LSAWRLLERFDRDQPEVRVYNPDYEKHGWQSTHTAVEVLHPDLPFLVDSVRMELNRRGYS 120
            L+AW+ L++   ++  V V+NPD E  GWQSTHT V +LHP++PFL+DS+R+ +N R   
Sbjct: 61   LAAWQFLQKRSAEETPVAVFNPDLESDGWQSTHTVVFILHPNIPFLIDSLRIAINHREIG 120

Query: 121  IHTLQTNVLSVRRSAKGELKEILPKGSQGKDVSQESLMYLEIDRCAHAGELRALEKAILE 180
             H++Q ++L V R   G+L+++     +      E+ + LEIDR ++  +LR LE  +  
Sbjct: 121  THSIQHSILQVNRDQNGKLEKLHTSKKKASGSDYEAFIVLEIDRHSNPEDLRDLEDTLQN 180

Query: 181  VLGEVRVTVADFEPMKAKARELLTWLGKAKLKVPAEELKEVRSYLEWLLDNHFTFLGYEE 240
            VL EVR+ V+DF  +  K  E+L  L      +  E+ +E R++LEWL  +HFTFLGY+E
Sbjct: 181  VLHEVRIAVSDFPVVTEKVNEILGELDNTTAGINEEQKEEARAFLEWLARDHFTFLGYDE 240

Query: 241  FSVADEADGGRMVYDEKSFLGLTRLLRAGLSKDDLHIEDYAVAY--LREPVLLSFAKAAH 298
            +  A +  G  +   E S LG+ R+      +  L+       +   R   +  FAK+A 
Sbjct: 241  YDFAKDKSGMVVRRVENSELGILRVNNERPDRVRLNELPQRTRHEMTRSDDIFIFAKSAQ 300

Query: 299  PSRVHRPAYPDYVSIRELDGKGRVIRECRFMGLFTSSVYNESVNDIPFIRGKVAEVMRRS 358
             SRVHRPAYPDY+++++ + KG V+ E RF+GL+T+ VYNE  ++IP +R K   VM+RS
Sbjct: 301  RSRVHRPAYPDYIAVKKFNSKGEVVGERRFLGLYTARVYNERPDEIPLLRRKFQSVMKRS 360

Query: 359  GFDTKAHLGKELAQVLEVLPRDDLFQTPVDELFSTALAIVRIQERNKIRVFLRKDPYGRF 418
            GF    + GKEL Q+L V PRD+LFQ   DEL   A +I+ IQER +I +FLR+D YG+F
Sbjct: 361  GFLRDDYAGKELEQILTVYPRDELFQIEQDELLKVAKSILYIQERRRIELFLREDVYGQF 420

Query: 419  CYCLAYVPRDVYSTETRLKIQQVLMERLQASDCEFWTFFSESVLARVQFILRVDPKSRID 478
              CLA+ PRD+Y+TE RLK++QVL++RL A D EF T FSESVLARVQF +RV       
Sbjct: 421  VTCLAFFPRDIYNTELRLKVEQVLVDRLGAEDVEFVTHFSESVLARVQFTIRVPQVENRQ 480

Query: 479  IDPARLEEEVIQACRSWQDDYSSLVVENLGEAKGTNVLADFPKGFPAGYRERFAPHFAVV 538
            +  A + E+VI+  +SW+D  S  + E  GE +G  +   +  GFPA Y + F+P  A +
Sbjct: 481  LPTAEIREKVIELAQSWRDGLSEALSEAWGEEQGNELYRLWAGGFPASYTDMFSPRRAAI 540

Query: 539  DLQHLLSLSEQRPLVMSFYQPLAQGEQQLHCKLYHADTPLALSDVLPILENLGLRVLGEF 598
            DL+H+ S +    L MSFY+ L + E  LH KL++ D PL LSDV+PI +NLG RV+GE 
Sbjct: 541  DLEHIASSANNHDLAMSFYRALEEDESTLHFKLFYPDEPLPLSDVMPIFDNLGFRVIGEH 600

Query: 599  PYRLRHQNGREYWIHDFAFTYAEGLDVDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTA 658
            P+ +  ++ +  WIHDF     +G  VDI ++  I ++ F  +  G+AENDAFNR++L++
Sbjct: 601  PFEVIDRHNKTVWIHDFTLQAHQGTVVDIHRIRPIFEELFRRVWYGEAENDAFNRMLLSS 660

Query: 659  NLPWRDVALLRAYARYLKQIRLGFDLGYIASALNAHTDIARELVRLFKTRFYLARKLTAE 718
             + WR++ALLR YARY++QIR      +I++ L  H ++ R L+  F+ RF   R  +  
Sbjct: 661  YMSWREIALLRTYARYMRQIRFSNSQTFISNTLVNHVELTRLLLEFFEIRFNPERYQSPG 720

Query: 719  DLEDKQQKLEQAILGALDEVQVLNEDRILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFK 778
              +  QQKLE      L+ V+ L+EDR+LR YL+LI+ATLRTN+YQ   +G  K Y S K
Sbjct: 721  KSQAAQQKLEIEFNAGLENVENLSEDRVLRLYLELIQATLRTNYYQHGESGGPKPYISVK 780

Query: 779  FNPKAIPELPRPVPKYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQ 838
            F+P  IP++P P+P +EIFVYSPRVEGVHLRGGKVARGGLRWSDR ED+RTE+LGLVKAQ
Sbjct: 781  FDPSRIPDMPLPMPMFEIFVYSPRVEGVHLRGGKVARGGLRWSDRFEDYRTEILGLVKAQ 840

Query: 839  QVKNAVIVPVGAKGGFVPRRLPLGGSRDEIQAEAIACYRIFISGLLDITDNLKEGEVVPP 898
            QVKNAVIVPVGAKGGFV +RLP    R+  QAE I  Y+ FI GLLDITDNL +  + PP
Sbjct: 841  QVKNAVIVPVGAKGGFVAKRLPDPSDREAFQAEGIEAYKTFIRGLLDITDNLVDAGIAPP 900

Query: 899  ANVVRHDEDDPYLVVAADKGTATFSDIANGIAAEYGFWLGDAFASGGSAGYDHKGMGITA 958
              V+RHD+DD YLVVAADKGTATFSDIANG+AAEYGFW+GDAFASGGS GYDHK MGITA
Sbjct: 901  ERVIRHDDDDHYLVVAADKGTATFSDIANGLAAEYGFWMGDAFASGGSNGYDHKKMGITA 960

Query: 959  KGAWVSVQRHFRERGIDVQKDNISVIGIGDMAGDVFGNGLLMSDKLQLVAAFNHMHIFID 1018
            +GAWVSV+RHFRE GI+   D  + IGIGDM GDVFGNG+L S+K +LVAAFNH+HIF+D
Sbjct: 961  RGAWVSVERHFREMGINPGLDEFTAIGIGDMGGDVFGNGMLCSEKTKLVAAFNHVHIFVD 1020

Query: 1019 PNPDAASSFVERQRLFNLPRSSWADYDAKLISAGGGIFLRSAKSIAITPEMKARFDIQAD 1078
            P+PD   S+ ER RLF LPRS+W DYD+KLIS GGG+F R++KSI ++PEMK    I++D
Sbjct: 1021 PSPDPEKSYKERMRLFGLPRSAWTDYDSKLISKGGGVFSRNSKSIPVSPEMKKLLGIKSD 1080

Query: 1079 RLAPTELIHALLKAPVDLLWNGGIGTYVKSSKETHADVGDKANDGLRVDGRELRAKVVGE 1138
            R+ P  LI  +LKA VDLLW GGIGTYVK++ E+H+DVGDKANDGLR++G +LR KVVGE
Sbjct: 1081 RVPPNMLISHILKAQVDLLWVGGIGTYVKAASESHSDVGDKANDGLRINGSDLRCKVVGE 1140

Query: 1139 GGNLGMTQLARVEFGLHGGANNTDFIDNAGGVDCSDHEVNIKILLNEVVQAGDMTEKQRN 1198
            GGNLG+TQL R+EF L GG  NTDFIDN+GGVDCSDHEVN+KILLN  V  GD+T KQRN
Sbjct: 1141 GGNLGLTQLGRIEFALKGGRLNTDFIDNSGGVDCSDHEVNMKILLNRAVAMGDLTNKQRN 1200

Query: 1199 ALLVKMTDAVGALVLGNNYKQTQALSLAQRRARERIAEYKRLMGDLEARGKLDRALEFLP 1258
             +L +MTD V  LVL NNY+QTQA+S+A   A  R+ EY+RLM   E+ GKL+RALEFLP
Sbjct: 1201 IMLEEMTDDVAELVLKNNYRQTQAISIASEDAATRLEEYRRLMNTFESEGKLNRALEFLP 1260

Query: 1259 SDEELAERISAGQGLTRAELSVLISYSKIDLKESLLKSLVPDDDYLTRDMETAFPALLAE 1318
             DE L+ER    +GLTR ELSVLISY K DLK++L+ S +PDD  L  +M   FP  L +
Sbjct: 1261 DDETLSERKLDKKGLTRPELSVLISYVKGDLKQTLIDSTLPDDPLLAGEMYKVFPRDLTQ 1320

Query: 1319 KFGDAMRRHRLKREIVSTQIANDLVNHMGITFVQRLKESTGMSAANVAGAYVIVRDVFHL 1378
            KF   +  H+L+REI++TQIAND+VNHMGITFV+RL +STG  AA++A A++I RDVF +
Sbjct: 1321 KFSKELGEHQLRREIIATQIANDMVNHMGITFVERLNQSTGADAASIALAWIIARDVFRI 1380

Query: 1379 PHWFRQIENLDYQVPADIQLTLMDELMRLGRRATRWFLRSRRNELDAARDVAHFGPRIAA 1438
             +W+ +IE LD+ V A +Q+ LM +LMRL RR+ RW LR+RR EL     +  F   + A
Sbjct: 1381 DNWWDRIEALDFHVSAQLQMELMQDLMRLMRRSVRWLLRNRRAELSIQHHMERFADSVWA 1440

Query: 1439 LGLKLNELLEGPTRELWQARYQTYVDAGVPELLARMVAGTSHLYTLLPIIEASDVTGQDT 1498
            +   L E L    +  W+ R+Q  VDAG+P  LA +V+GT HLY+ L IIEA + +G   
Sbjct: 1441 ITAGLPEYLGDQAKTTWEKRHQALVDAGLPSELASVVSGTGHLYSSLGIIEAHEASGMPL 1500

Query: 1499 AEVAKAYFAVGSALDLTWYLQQITNLPVENNWQALAREAFRDDLDWQQRAITVSVLQMQD 1558
              VA  Y+ +G  LDL W+   I +L   ++WQALARE+FR+DLDWQQRA+T  VL++ D
Sbjct: 1501 KTVANLYYELGDRLDLNWFASAIASLQPGSHWQALARESFREDLDWQQRALTTGVLKLAD 1560

Query: 1559 GPKEVEARVGLWLEQHLPLVERWRAMLVELRAASGTDYAMYAVANRELMDLAQSSQH 1615
             P++V A V  WL +H  +++RW++ML EL+     +YAM++VA REL+DLAQS+ H
Sbjct: 1561 KPEDVPACVEAWLSRHQQMIDRWKSMLSELKGVREPEYAMFSVALRELLDLAQSTMH 1617


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: 6101
Number of extensions: 265
Number of successful extensions: 2
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: 1628
Length adjustment: 52
Effective length of query: 1568
Effective length of database: 1576
Effective search space:  2471168
Effective search space used:  2471168
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