Alignments for a candidate for gdhA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Shewanella oneidensis MR-1

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate 201733 SO2593 conserved hypothetical protein (NCBI ptt file)

Query= SwissProt::Q9HZE0
         (1620 letters)



>FitnessBrowser__MR1:201733
          Length = 1614

 Score = 1450 bits (3753), Expect = 0.0
 Identities = 772/1582 (48%), Positives = 1036/1582 (65%), Gaps = 14/1582 (0%)

Query: 31   QVTLFAEQFFSLISLDELTQRRLSDLVGCTLSAWRLLERFDRDQPEVRVYNPDYEKHGWQ 90
            QV  FA   ++ +S D+L  R  SDL G  LS W  L +  + +  +RV+NP   KHGWQ
Sbjct: 30   QVEQFATCLYAHMSKDDLNARNDSDLYGAVLSLWNALNKTPKGETHLRVFNPSQSKHGWQ 89

Query: 91   STHTAVEVLHPDLPFLVDSVRMELNRRGYSIHTLQTNVLSVRRSAKGELKEILPKGSQGK 150
            STH+ +EV+ PD+PFLVDSV M LNR G + H +    L++ RSA+ E+ ++        
Sbjct: 90   STHSIIEVIQPDMPFLVDSVGMALNRMGITAHVMLHTPLAIERSAQ-EVTKVTYLNQSPD 148

Query: 151  DVSQESLMYLEIDRCAHAGELRALEKAILEVLGEVRVTVADFEPMKAKARELLTWLGKAK 210
                 ++  +EIDR +   +++ALE+ I  VL +V  +V D+  M AK  E +  L K  
Sbjct: 149  STEHVAVFLIEIDRQSSTADIKALEREIQSVLADVAASVNDWGAMSAKLSETIKELPKRP 208

Query: 211  LKVPAEELKEVRSYLEWLLDNHFTFLGYEEFSVADEADGGRMVYDEKSFLGLTRLLRAGL 270
                 +EL+E  ++L +L ++HFT LGY ++ +        +V +  S LGL        
Sbjct: 209  FPGEKQELEEAINFLTYLNNHHFTLLGYRQYDLKRVEGDVELVPNIASSLGLMNKHHKTQ 268

Query: 271  SKDDLHIEDYAVAYLREPV---LLSFAKAAHPSRVHRPAYPDYVSIRELDGKGRVIRECR 327
             +  L +  ++ +  +E +   LL   K++  SRVHRPAY DY+ I+  D KG VI E R
Sbjct: 269  PEQGLLLSSFSDSARKEALDHSLLILTKSSAKSRVHRPAYVDYIGIKRFDKKGNVIGEDR 328

Query: 328  FMGLFTSSVYNESVNDIPFIRGKVAEVMRRSGFDTKAHLGKELAQVLEVLPRDDLFQTPV 387
            F+GL+ S+VYN S  +IP +  KV  V+ RSG   ++H  K L  +LE LPRD+L Q  V
Sbjct: 329  FIGLYASNVYNRSPREIPLLNEKVQRVLDRSGLTPRSHDYKALLNILENLPRDELIQANV 388

Query: 388  DELFSTALAIVRIQERNKIRVFLRKDPYGRFCYCLAYVPRDVYSTETRLKIQQVLMERLQ 447
            D+L  TA  ++ +Q+R+K+++F+RKD +GRF  CL YV +D Y+T+ R   Q++L +   
Sbjct: 389  DDLAHTAHGVLEMQDRDKLKLFVRKDGFGRFLSCLVYVSKDRYNTKLRQDTQRILAQHFN 448

Query: 448  AS-DCEFWTFFSESVLARVQFILRVDPKSRIDIDPARLEEEVIQACRSWQDDYSSLVVEN 506
            +  D EF T+FSES LAR  +I++VD  + +D+D A +E  +I+A RSW+D  ++ +   
Sbjct: 449  SKEDVEFTTYFSESTLARTHYIVKVD-NNNMDVDVAAIENNLIEAARSWEDKLNTALNNA 507

Query: 507  LGEAKGTNVLADFPKGFPAGYRERFAPHFAVVDLQHLLSLSEQRPLVMSFYQP--LAQGE 564
            LGE  GT+++  +   F   Y+E   P  AVVD+Q L +L ++  L M FYQP   A  +
Sbjct: 508  LGEEAGTHLMKRYANAFEQSYKEDVLPSSAVVDMQQLEALDDEHKLGMLFYQPQEAALND 567

Query: 565  QQLHCKLYHADTPLALSDVLPILENLGLRVLGEFPYRLRHQNGREYWIHDFAFTYAEGLD 624
             ++  KL+H D P+ LSDVLP+LEN GLRV+ E PY +   +G  +WI DF  T      
Sbjct: 568  NKVRLKLFHKDEPIHLSDVLPMLENFGLRVINERPYEVTTADGSTFWILDFLMTVKVVNT 627

Query: 625  VDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTANLPWRDVALLRAYARYLKQIRLGFDL 684
             +I    +  Q A   +     E+D FNR++L + L  R+V++LRAYA+Y++QI   F  
Sbjct: 628  DNIADSQDRFQTALSQVWQKKLEDDGFNRIILASGLTGREVSVLRAYAKYMRQIDATFSQ 687

Query: 685  GYIASALNAHTDIARELVRLFKTRFYLARKLTAEDLEDKQQKLEQAILGALDEVQVLNED 744
             YI      +  IA  LV++F  +F    KL    L     K  + I   LDEV  L++D
Sbjct: 688  AYIEETFGRYPQIADLLVKMFIRKFN--PKLKTRTLG----KFMEQINLRLDEVSSLDDD 741

Query: 745  RILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFKFNPKAIPELPRPVPKYEIFVYSPRVE 804
            RI+RRYLDLI ATLRTNFYQ D  G++KSY SFKF P  IPE+PRP+PK+EIFVYSPRVE
Sbjct: 742  RIIRRYLDLINATLRTNFYQLDAKGESKSYISFKFMPSLIPEMPRPLPKFEIFVYSPRVE 801

Query: 805  GVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQQVKNAVIVPVGAKGGFVPRRLPLGGS 864
            GVHLR GKVARGGLRWSDR EDFRTEVLGLVKAQQVKN VIVPVGAKGGFV ++LP  G 
Sbjct: 802  GVHLRYGKVARGGLRWSDRREDFRTEVLGLVKAQQVKNTVIVPVGAKGGFVCKQLPTEGG 861

Query: 865  RDEIQAEAIACYRIFISGLLDITDNLKEGEVVPPANVVRHDEDDPYLVVAADKGTATFSD 924
            R+    E   CYRIFI  LLDITDN+  GE+V P +VVRHDEDDPYLVVAADKGTATFSD
Sbjct: 862  REAFFTEGQECYRIFIRALLDITDNILNGEIVHPVDVVRHDEDDPYLVVAADKGTATFSD 921

Query: 925  IANGIAAEYGFWLGDAFASGGSAGYDHKGMGITAKGAWVSVQRHFRERGIDVQKDNISVI 984
            IAN I+ EY FWLGDAFASGGS GYDHK MGITAKG W SV+RHFRE GID Q  + + +
Sbjct: 922  IANSISLEYNFWLGDAFASGGSNGYDHKKMGITAKGGWESVKRHFREVGIDCQTTDFTCL 981

Query: 985  GIGDMAGDVFGNGLLMSDKLQLVAAFNHMHIFIDPNPDAASSFVERQRLFNLPRSSWADY 1044
            GIGDMAGDVFGNG+L+S   +LVAAFNHMHIFIDPNPDAA+S+ ER RLF LPRSSW DY
Sbjct: 982  GIGDMAGDVFGNGMLLSKHTKLVAAFNHMHIFIDPNPDAATSYEERARLFALPRSSWEDY 1041

Query: 1045 DAKLISAGGGIFLRSAKSIAITPEMKARFDIQADRLAPTELIHALLKAPVDLLWNGGIGT 1104
            ++KLIS GGG+FLRS+KSI ++ EMK     +   + PTE++  LLK PVDL+WNGGIGT
Sbjct: 1042 NSKLISKGGGVFLRSSKSIPLSAEMKQMLGTEKISMTPTEMMKELLKMPVDLIWNGGIGT 1101

Query: 1105 YVKSSKETHADVGDKANDGLRVDGRELRAKVVGEGGNLGMTQLARVEFGLHGGANNTDFI 1164
            YVKSS+ET+A+VGD+AND LRV+GRELRAK+VGEGGNLG TQL R+E+  +GG  NTDF+
Sbjct: 1102 YVKSSRETNAEVGDRANDALRVNGRELRAKIVGEGGNLGCTQLGRIEYAANGGRINTDFV 1161

Query: 1165 DNAGGVDCSDHEVNIKILLNEVVQAGDMTEKQRNALLVKMTDAVGALVLGNNYKQTQALS 1224
            DN GGVDCSD+EVNIKILLN +V  G++T KQRN LL +MT+ VG +VL +   QT+ +S
Sbjct: 1162 DNVGGVDCSDNEVNIKILLNAMVTEGELTLKQRNRLLGEMTEEVGEIVLQDCKDQTRTIS 1221

Query: 1225 LAQRRARERIAEYKRLMGDLEARGKLDRALEFLPSDEELAERISAGQGLTRAELSVLISY 1284
            + Q R  E++ E  R +  LE  GKLDRALEFLPS+EEL ER++ G+ LTR ELSVL++Y
Sbjct: 1222 VTQVRGAEQLKEQIRFIQYLEKEGKLDRALEFLPSEEELTERLANGRALTRPELSVLVAY 1281

Query: 1285 SKIDLKESLLKSLVPDDDYLTRDMETAFPALLAEKFGDAMRRHRLKREIVSTQIANDLVN 1344
            +K+ LKE LL   + +D  L++ +   FP  L E +   M  H L+ EI++T +AN+LVN
Sbjct: 1282 AKMVLKEQLLTPEITEDTLLSQLLIAYFPKKLQELYSARMVTHPLRGEIIATSLANELVN 1341

Query: 1345 HMGITFVQRLKESTGMSAANVAGAYVIVRDVFHLPHWFRQIENLDYQVPADIQLTLMDEL 1404
             MG+ FVQR+++ TG S A+ A  Y + R+VF L    + I +L+  VPA +Q  ++ +L
Sbjct: 1342 DMGLNFVQRMQDETGASVADAAICYTMAREVFGLAELTKSITDLNGIVPAVVQGEMLHQL 1401

Query: 1405 MRLGRRATRWFLRSRRNELDAARDVAHFGPRIAALGLKLNELLEGPTRELWQARYQTYVD 1464
             R  RRA RWFLR R       + VA F P    L   ++  L        QA     + 
Sbjct: 1402 RRNMRRACRWFLRHRNRSWSIEQTVAFFKPVFEQLKANVHSYLAEEEAAGIQAEINALIK 1461

Query: 1465 AGVPELLARMVAGTSHLYTLLPIIEASDVTGQDTAEVAKAYFAVGSALDLTWYLQQITNL 1524
              VP+ +A  VA  S L++ L I + +    +  A VA+ YF +G+ ++L W+L+QI+  
Sbjct: 1462 ENVPQDVASTVANMSTLFSTLDIAQIAQAEEKTVALVAETYFKLGARVELHWFLEQISAQ 1521

Query: 1525 PVENNWQALAREAFRDDLDWQQRAITVSVLQMQDGPKEVEARVGLWLEQHLPLVERWRAM 1584
            PV N+WQALAR AFR++LDWQQRA+T  VL+        ++ + LW+E +  L+ERW  M
Sbjct: 1522 PVTNHWQALARAAFREELDWQQRALTSVVLRTCSATCNAQSVISLWIETNQALLERWFHM 1581

Query: 1585 LVELRAASGTDYAMYAVANREL 1606
            L + + +   ++A ++VA REL
Sbjct: 1582 LADFKTSQNHEFAKFSVALREL 1603


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: 5605
Number of extensions: 242
Number of successful extensions: 8
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: 1614
Length adjustment: 51
Effective length of query: 1569
Effective length of database: 1563
Effective search space:  2452347
Effective search space used:  2452347
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