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

GapMind for catabolism of small carbon sources

Aligments 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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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, or view the source code.

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