Alignments for a candidate for gdhA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Shewanella sp. ANA-3

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate 7024607 Shewana3_1785 glutamate dehydrogenase (NAD) (RefSeq)

Query= SwissProt::Q9HZE0
         (1620 letters)



>FitnessBrowser__ANA3:7024607
          Length = 1614

 Score = 1451 bits (3755), Expect = 0.0
 Identities = 772/1583 (48%), Positives = 1042/1583 (65%), Gaps = 16/1583 (1%)

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+   K  +   +Q  
Sbjct: 90   STHSIIEVIQPDMPFLVDSVGMALNRMGITAHMMLHTPLAIERSAQDVTK--VTYLNQSP 147

Query: 151  DVSQESLMYL-EIDRCAHAGELRALEKAILEVLGEVRVTVADFEPMKAKARELLTWLGKA 209
            D ++   ++L EIDR + + +++ALE+ I  VLG+V  +V D+  M AK  E +  L K 
Sbjct: 148  DSTEHVAVFLIEIDRQSSSVDIKALEREIQSVLGDVAASVNDWSAMSAKLSETIKELPKR 207

Query: 210  KLKVPAEELKEVRSYLEWLLDNHFTFLGYEEFSVADEADGGRMVYDEKSFLGLTRLLRAG 269
                  +EL+E  ++L +L ++HFT LGY ++ +        +V +  S LGL       
Sbjct: 208  PFPGEKQELEEAINFLTYLNNHHFTLLGYRQYDLKRVEGDVELVPNMASSLGLMNKHHKT 267

Query: 270  LSKDDLHIEDYAVAYLREPV---LLSFAKAAHPSRVHRPAYPDYVSIRELDGKGRVIREC 326
              +  L +  ++ +  +E +   LL   K++  SRVHRPAY DY+ I+  D KG V+ E 
Sbjct: 268  QPEQGLLLSSFSDSARKEALDHSLLILTKSSAKSRVHRPAYVDYIGIKRFDKKGNVVGED 327

Query: 327  RFMGLFTSSVYNESVNDIPFIRGKVAEVMRRSGFDTKAHLGKELAQVLEVLPRDDLFQTP 386
            RF+GL+ S+VYN S  +IP +  KV  V+ RSG   ++H  K L  +LE LPRD+L Q  
Sbjct: 328  RFIGLYASNVYNRSPREIPLLNEKVQRVLDRSGLTPRSHDYKALLNILENLPRDELIQAN 387

Query: 387  VDELFSTALAIVRIQERNKIRVFLRKDPYGRFCYCLAYVPRDVYSTETRLKIQQVLMERL 446
            VD+L  TA  ++ +Q+R+K+++F+RKD +GRF  CL YV +D Y+T+ R   Q++L +  
Sbjct: 388  VDDLAHTAHGVLEMQDRDKLKLFVRKDGFGRFLSCLVYVSKDRYNTKLRQDTQRILAQHF 447

Query: 447  QAS-DCEFWTFFSESVLARVQFILRVDPKSRIDIDPARLEEEVIQACRSWQDDYSSLVVE 505
             +  D EF T+FSES LAR  +I++VD  + +D+D A +E  +I+A RSW+D  ++ +  
Sbjct: 448  NSKEDVEFTTYFSESTLARTHYIVKVD-NNNMDVDVAAIENNLIEAARSWEDKLNTALNT 506

Query: 506  NLGEAKGTNVLADFPKGFPAGYRERFAPHFAVVDLQHLLSLSEQRPLVMSFYQP--LAQG 563
             LGE  GT+++  +   F   Y+E   P  AVVD+Q L +L ++  L M FYQP   A  
Sbjct: 507  ALGEEAGTHLMKRYANAFEQSYKEDVLPSSAVVDMQQLEALDDEHKLGMLFYQPQEAALN 566

Query: 564  EQQLHCKLYHADTPLALSDVLPILENLGLRVLGEFPYRLRHQNGREYWIHDFAFTYAEGL 623
            + ++  KL+H D P+ LSDVLP+LEN GLRV+ E PY +   +G  +WI DF  T     
Sbjct: 567  DNKVRLKLFHKDEPIHLSDVLPMLENFGLRVINERPYEVTTSDGSTFWILDFLMTVKVTN 626

Query: 624  DVDIQQLNEILQDAFVHIVSGDAENDAFNRLVLTANLPWRDVALLRAYARYLKQIRLGFD 683
              +I    +  Q A   +     E+D FNR++L + L  R+V++LRAYA+Y++QI   F 
Sbjct: 627  TDNIADSQDRFQTALSQVWQKKLEDDGFNRIILASGLTGREVSVLRAYAKYMRQIDATFS 686

Query: 684  LGYIASALNAHTDIARELVRLFKTRFYLARKLTAEDLEDKQQKLEQAILGALDEVQVLNE 743
              YI      +  IA  LV++F  +F    KL    L     K  + I   LDEV  L++
Sbjct: 687  QAYIEETFGRYPQIADLLVKMFIRKFN--PKLKTRTLG----KFMEQINLRLDEVSSLDD 740

Query: 744  DRILRRYLDLIKATLRTNFYQPDGNGQNKSYFSFKFNPKAIPELPRPVPKYEIFVYSPRV 803
            DRI+RRYLDLI ATLRTNFYQ D  G++KSY SFKF P  IPE+PRP+PK+EIFVYSPRV
Sbjct: 741  DRIIRRYLDLINATLRTNFYQLDAKGESKSYISFKFMPSLIPEMPRPLPKFEIFVYSPRV 800

Query: 804  EGVHLRGGKVARGGLRWSDREEDFRTEVLGLVKAQQVKNAVIVPVGAKGGFVPRRLPLGG 863
            EGVHLR GKVARGGLRWSDR EDFRTEVLGLVKAQQVKN VIVPVGAKGGFV ++LP  G
Sbjct: 801  EGVHLRYGKVARGGLRWSDRREDFRTEVLGLVKAQQVKNTVIVPVGAKGGFVCKQLPTEG 860

Query: 864  SRDEIQAEAIACYRIFISGLLDITDNLKEGEVVPPANVVRHDEDDPYLVVAADKGTATFS 923
             R+    E   CYRIFI  LLDITDN+  GE+V P +VVRHDEDDPYLVVAADKGTATFS
Sbjct: 861  GREAFFTEGQECYRIFIRALLDITDNIVNGEIVHPVDVVRHDEDDPYLVVAADKGTATFS 920

Query: 924  DIANGIAAEYGFWLGDAFASGGSAGYDHKGMGITAKGAWVSVQRHFRERGIDVQKDNISV 983
            DIAN I+ EY FWLGDAFASGGS GYDHK MGITA+G W SV+RHFRE GID Q  + S 
Sbjct: 921  DIANAISQEYNFWLGDAFASGGSNGYDHKKMGITARGGWESVKRHFREVGIDCQTTDFSC 980

Query: 984  IGIGDMAGDVFGNGLLMSDKLQLVAAFNHMHIFIDPNPDAASSFVERQRLFNLPRSSWAD 1043
            +GIGDMAGDVFGNG+L+S   +LVAAFNHMHIF+DPNPD A+S+ ER RLF LPRS+W D
Sbjct: 981  LGIGDMAGDVFGNGMLLSKHTKLVAAFNHMHIFVDPNPDTAASYEERARLFALPRSTWED 1040

Query: 1044 YDAKLISAGGGIFLRSAKSIAITPEMKARFDIQADRLAPTELIHALLKAPVDLLWNGGIG 1103
            Y++KLIS GGGIFLRS+KSI ++ EMK   + +   + PTEL+  LLK PVDL+WNGGIG
Sbjct: 1041 YNSKLISKGGGIFLRSSKSIPLSAEMKQMLETEKTSMTPTELMKELLKMPVDLIWNGGIG 1100

Query: 1104 TYVKSSKETHADVGDKANDGLRVDGRELRAKVVGEGGNLGMTQLARVEFGLHGGANNTDF 1163
            TYVKSS+ETHA+VGD+AND LRV+GRELRAK+VGEGGNLG TQL R+E+  +GG  NTDF
Sbjct: 1101 TYVKSSRETHAEVGDRANDALRVNGRELRAKIVGEGGNLGCTQLGRIEYAANGGRINTDF 1160

Query: 1164 IDNAGGVDCSDHEVNIKILLNEVVQAGDMTEKQRNALLVKMTDAVGALVLGNNYKQTQAL 1223
            +DN GGVDCSD+EVNIKILLN +V  G++T KQRN LL +MT+ VG +VL +   QT+ +
Sbjct: 1161 VDNVGGVDCSDNEVNIKILLNALVAEGELTLKQRNRLLEEMTEEVGQIVLQDCKDQTRTI 1220

Query: 1224 SLAQRRARERIAEYKRLMGDLEARGKLDRALEFLPSDEELAERISAGQGLTRAELSVLIS 1283
            S+ Q R  E++ E  R +  LE  GKLDRALEFLPS+EELAER++ G+ LTR ELSVL++
Sbjct: 1221 SVTQVRGAEQLKEQIRFIQYLEKEGKLDRALEFLPSEEELAERLANGRALTRPELSVLVA 1280

Query: 1284 YSKIDLKESLLKSLVPDDDYLTRDMETAFPALLAEKFGDAMRRHRLKREIVSTQIANDLV 1343
            Y+K+ LKE LL   + +D  L++ +   FP  L E +   M  H L+ EI++T +AN+LV
Sbjct: 1281 YAKMVLKEQLLTQEITEDTLLSQLLIAYFPKQLQELYSHRMVTHPLRGEIIATSLANELV 1340

Query: 1344 NHMGITFVQRLKESTGMSAANVAGAYVIVRDVFHLPHWFRQIENLDYQVPADIQLTLMDE 1403
            N MG+ FVQR+++ TG S A+ A  Y + R+VF L    + I +L+  VPA +Q  ++ +
Sbjct: 1341 NDMGLNFVQRMQDETGASVADAAICYTMAREVFGLAELTKAITDLNGIVPAVVQGEMLHQ 1400

Query: 1404 LMRLGRRATRWFLRSRRNELDAARDVAHFGPRIAALGLKLNELLEGPTRELWQARYQTYV 1463
            L R  RRA RWFLR R       + VA F P    +   ++  L        QA     +
Sbjct: 1401 LRRNMRRACRWFLRHRNRTWSIEQTVAFFKPVFEQIKANVHSYLVEEEAAGIQAEINALI 1460

Query: 1464 DAGVPELLARMVAGTSHLYTLLPIIEASDVTGQDTAEVAKAYFAVGSALDLTWYLQQITN 1523
               VP+ +A +VA  S L++ L I + +    +    VA+ YF +G+ ++L W+L+QI+ 
Sbjct: 1461 KENVPQEVATVVANMSTLFSALDIAQIAQAEEKTVELVAETYFKLGARVELHWFLEQISA 1520

Query: 1524 LPVENNWQALAREAFRDDLDWQQRAITVSVLQMQDGPKEVEARVGLWLEQHLPLVERWRA 1583
             PV N+WQALAR AFR++LDWQQRA+T  VL+      + ++ +  W++ +  L+ERW  
Sbjct: 1521 QPVANHWQALARAAFREELDWQQRALTSVVLRTCSETCDAQSVISQWIDTNQALLERWFH 1580

Query: 1584 MLVELRAASGTDYAMYAVANREL 1606
            ML + + +   ++A ++VA REL
Sbjct: 1581 MLADFKTSQSHEFAKFSVALREL 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: 5604
Number of extensions: 242
Number of successful extensions: 9
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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