GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Shewanella loihica PV-4

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate 5209331 Shew_1809 NAD-glutamate dehydrogenase (RefSeq)

Query= SwissProt::E1V4J5
         (1613 letters)



>FitnessBrowser__PV4:5209331
          Length = 1614

 Score = 1449 bits (3750), Expect = 0.0
 Identities = 754/1600 (47%), Positives = 1067/1600 (66%), Gaps = 16/1600 (1%)

Query: 13   LLKQLKERLQSRLDKDKAAEVDTFAHLFYAAVPLEDLADRRLDDLYGATLSVWHFIQQFD 72
            LL+ +   + S++   +A +V+ FA   YA +  +DL  R   DLYGA LS+W+   +  
Sbjct: 11   LLENVVSLIHSKVPNTQAKQVEQFATCIYAHMSKDDLQHRNDSDLYGAVLSLWNAANKTP 70

Query: 73   PEAPKVRVLNPDFEEHGWQSTHTFIAVLHEDMPFLVDSVRVELNRRGMTVHAIHNAVLAV 132
                 +RV NP   +HGW+S+H+ I V+  DMPFLVDSV + LNR G+T H + +  L V
Sbjct: 71   VGETHIRVFNPSQSKHGWKSSHSIIEVIQPDMPFLVDSVGMALNRMGITTHMMLHTPLTV 130

Query: 133  GRDDEHRLQRVASPEETDAPEARESLIAIEVDRHSNPAELEEIEASLLEVLREVRTAVSD 192
             RD +  +  V+  ++ D    + ++  IEVDR S+ A+++ +E  +  VL +V  +V+D
Sbjct: 131  KRD-QGVITGVSYNDDKDESNDKVAVFLIEVDRLSSDADIKSLEKEIQSVLGDVAASVND 189

Query: 193  FDPMRAQARAAIEELEATRPAQVDPADHREAIEFLQWLLQDNFTFLGYDEYEVREDQGRQ 252
            +  M  +    I EL + RP   +  +  EAI FL +L   +FT LGY  Y++ + +G  
Sbjct: 190  WQAMSNKLSETIAELPS-RPFPGEKRELDEAINFLTYLNNHHFTLLGYRRYDLHKVEGDL 248

Query: 253  RLDKVQNSELGVFRLD-QPRYRERIR-TDLGVEGDHYVPMPQLMSFAKSAHHARIHRPTY 310
             L     + LG+  +  +P+  + +  + L            L+   KS   +R+HRP Y
Sbjct: 249  ELLPANETSLGLMNVPGKPKSSKGLMLSSLSDTARKEALDSSLLILTKSTEKSRVHRPAY 308

Query: 311  PDYISIDRYDDQGRVIGERRFLGMFTATVYNESPRNVPILRRKLQAVMDIAGFSPKGHNG 370
             DYI I R+D+QG VIGE RF+G++ + +YN SPR +P+L  K+Q V+D +G +P  H+ 
Sbjct: 309  VDYIGIKRFDEQGNVIGEDRFIGLYASNLYNRSPREIPLLAEKIQRVLDDSGLTPHSHDY 368

Query: 371  KQLLQILEVYPRDDLFQIDIEELAQTALGILDIRERRRVRLFIREDTFGKFYSCLVFVPR 430
            K L+ ILE  PRD++ Q    ELA  A G+L++++R +++LF+R+D FG+F SCLV+V +
Sbjct: 369  KALMHILETLPRDEIVQARESELASMAHGVLEMQDRDKLKLFVRKDGFGRFLSCLVYVSK 428

Query: 431  DVFSTELRVRLQELLCEELDATFG-DFNTYLSESVLARIQFILRFNGEKPVEYDIKRLEE 489
            D ++T+LR   Q +L +  +     +F TY SES LAR  +I++ +     + D+  +E 
Sbjct: 429  DRYNTKLREDTQRILAQHFNTKEDVEFTTYFSESTLARTHYIVKVDNNI-TDVDVAAIEN 487

Query: 490  KLVKLARNWRDDLLNASIEGFGEESANLLMSRFRDAFPASYREDFSARTAVYDLQHIGEL 549
             L++ AR+W D L  A I   GEES N L+ R+ +AFP SY+ED    +AV D++H+  L
Sbjct: 488  NLIEAARSWEDKLNTALITAQGEESGNRLVKRYVNAFPRSYKEDVLPSSAVVDIEHLEAL 547

Query: 550  DEGAPLALSLYRLIEE--EGSGVNLKLFHRGAPIPLSDVLPMMENLGLRVIGERPYEVQA 607
            D+   L +  Y+  E   + + V LKLFH+  PI LSDVLPM+EN GLRVI ERPYEV  
Sbjct: 548  DDDHKLGMLFYQPQETALKDNKVRLKLFHKDEPIHLSDVLPMLENFGLRVINERPYEVMT 607

Query: 608  SDAS-YWIHDFNLEHHTSVEMNLQEMRGPFIEAFQRIWAGEADNDAFNRLIIGANLDWRE 666
            +D S +WI DF +    +   NL + +  F  A  ++W  E ++D FNRL++   L  RE
Sbjct: 608  ADGSTFWILDFLMTVQGAAVDNLADSQDRFQTALSQVWRKELEDDGFNRLVLATGLSGRE 667

Query: 667  VAMLRAYARYLKQIRFGMSQDYIATTLGSHPEITRELVSLFELRFDPA--ERPGEGDIEE 724
            V++LRAYA+Y++QI    SQ YI  T  S+P+I   LV +F  +F+P    R     +E+
Sbjct: 668  VSVLRAYAKYMRQIDATFSQAYIEETFSSYPQIADLLVKMFIRKFNPKLKTRTLAKFVEQ 727

Query: 725  CESRILTLLDEVPSLNDDQLLRRYMELIKATLRTNYYQRTEEGRYKDYLAFKLDPSQVSG 784
             + R    L++V SL+DD+++RRY++LI ATLRTN+YQ   +G  K Y++FK  P ++  
Sbjct: 728  IDMR----LEDVSSLDDDRIIRRYLDLINATLRTNFYQVLPDGSNKPYVSFKFSPEEIPE 783

Query: 785  IPKPCPAYEIFVCSPRVEGVHLRGGKVARGGLRWSDRHEDFRTEVLGLVKAQQVKNAVIV 844
            +P+P P +EIFV SPRVEGVHLRGGKVARGGLRWSDR EDFRTEVLGLVKAQQVKN VIV
Sbjct: 784  MPRPLPKFEIFVYSPRVEGVHLRGGKVARGGLRWSDRREDFRTEVLGLVKAQQVKNTVIV 843

Query: 845  PMGAKGGFVCKRMPEGADREATQKEGIACYQIFIRALLDVTDNLVGGEVVPPRDVVRHDD 904
            P+GAKGGFVCK++P    R+A   EG  CY++FIR LLD++DN+V GE+VPP +VVRHD+
Sbjct: 844  PVGAKGGFVCKQLPTEGGRDAFFTEGQECYRLFIRGLLDISDNIVEGEIVPPANVVRHDE 903

Query: 905  NDPYLVVAADKGTATFSDIANEISTEYGHWLGDAFASGGANGYDHKKMAITAKGAWESVK 964
            +DPYLVVAADKGTATFSDIAN IS EYG WLGDAFASGG+NGYDHKKM ITA+GAWESVK
Sbjct: 904  DDPYLVVAADKGTATFSDIANAISEEYGFWLGDAFASGGSNGYDHKKMGITARGAWESVK 963

Query: 965  RHFRGLGVNTQEDEFSVVGIGDMAGDVFGNGMLLSDKIRLVGAFNHLHIFVDPTPDAAAS 1024
            RHFR +GV+ Q  +F+ + IGDMAGDVFGNGMLLS+  RLV AFNH+HIF+DP PDAA+S
Sbjct: 964  RHFREIGVDCQTTDFTCLAIGDMAGDVFGNGMLLSEHTRLVTAFNHMHIFIDPNPDAASS 1023

Query: 1025 FAERQRLFDMPRSSWEDYNTELISEGGGIFPRSAKSITITPQMKKVFGIREDKLSPNELI 1084
            + ER RLF+MPRSSWEDYN +LIS+GGGIF RSAKSIT+TP+MKK+   ++  ++PNEL+
Sbjct: 1024 YKERARLFEMPRSSWEDYNKDLISKGGGIFLRSAKSITLTPEMKKMLDTKKASMTPNELL 1083

Query: 1085 RAMLVSKVDLVWNGGIGTYVKSSEETDAEVGDKANDALRIDGRELNCRVVGEGGNLGLTQ 1144
            + +L  KVDL+WNGGIGTY+K++ ET AEVGD+ANDALR++G E+  R++GEGGNLG TQ
Sbjct: 1084 KELLKMKVDLIWNGGIGTYIKATSETHAEVGDRANDALRVNGNEVQARIIGEGGNLGCTQ 1143

Query: 1145 RGRMEAAAKGVRVNTDFIDNAGGVNCSDHEVNIKILIDEVVSRGDLTEKQRNQLLADMTD 1204
             GR+E AA G R+NTDF+DN GGV+CSD+EVNIKIL++ +V+ G++T KQRN+LL +MTD
Sbjct: 1144 LGRIEYAANGGRMNTDFVDNVGGVDCSDNEVNIKILLNAMVAEGEMTVKQRNRLLVEMTD 1203

Query: 1205 EVSELVLLDNYRQTQALDLAELLSRQGIGPYRRFISELEAAGQIDRELEFLPSDEELLER 1264
            EVS +VL D   QT+ + + ++   + +    RFI  LE   ++DR LEFLP+D+EL ER
Sbjct: 1204 EVSRIVLQDCKDQTRTISVTQVRGAEQLKEQIRFIHYLEKEDKLDRALEFLPTDDELAER 1263

Query: 1265 TQHNQGMTLPELSVLISYAKSVLKGDLIASDVPDDPTIMRFVERVFPSMLAERYRDEMYE 1324
              + + +T PELSVL++YAK VLK  L+  ++ DD  + + +   FP  L E+Y + M  
Sbjct: 1264 LANGKSLTRPELSVLVAYAKMVLKEQLLTPEITDDSFLSQLLIEYFPRQLQEKYSERMVT 1323

Query: 1325 HRLKREIVATQVANDLVDYMGVVFVRRLMDSTGADRADIARAYVIARDSFQLPRLWEQIE 1384
            H L+ EI+AT +AN+LV+ MG+ FV+R+ D TGA  A+ A  Y +AR+ F L  L + I 
Sbjct: 1324 HPLRAEIIATSLANELVNDMGLNFVQRMQDETGASVAEAAICYTMAREVFGLAELTKSIT 1383

Query: 1385 ALDNKVPSQVQYSMMLDLMRMLRRSTRWFLRQRT-GMSTRDTIDYFAPRLAQLQENIGKR 1443
            AL+  VP+ VQ  M+  L R LRR+ RWFLR R    S    + +F+P   +L++N+ + 
Sbjct: 1384 ALNGVVPAVVQGEMLHQLRRNLRRACRWFLRHRNRNQSIEQVVAFFSPVFQELRQNVHQY 1443

Query: 1444 LRGEEQEQWSARRQELVKAGVPEALASTVAAAGSLYAALGIIQTARQTDEKPQRVAEIFY 1503
            L  +E     A    LVK GVPE +A+ V    +L++AL I Q A   D+    VAE +Y
Sbjct: 1444 LVEDEVNGIRAEIAALVKEGVPEQVATDVVNMSTLFSALDISQIAELEDKPVALVAETYY 1503

Query: 1504 EVGARLELPWIIQQVTRLEVRDGWQAKARDTFRDDIDRQQLALTASVLGMDGGPRDSAER 1563
            ++GAR++L W ++Q++   V + WQA AR  FR+++D QQ +L++ VL       ++   
Sbjct: 1504 KLGARIDLHWFLEQISAQPVANHWQALARAAFREELDWQQRSLSSVVLRTCPSVCEADAI 1563

Query: 1564 VDRWLSLHEGMHQRWRHLLEEVGSGSQGGFPLFAVAVREL 1603
            +D+W+  ++G+ +RW H+L +  +     F  F+VA+REL
Sbjct: 1564 IDQWVESNQGLLERWFHMLADFKTSQTHEFAKFSVALREL 1603


Lambda     K      H
   0.320    0.137    0.400 

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: 5570
Number of extensions: 263
Number of successful extensions: 11
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: 1613
Length of database: 1614
Length adjustment: 51
Effective length of query: 1562
Effective length of database: 1563
Effective search space:  2441406
Effective search space used:  2441406
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 (21.8 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