Alignments for a candidate for gdhA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Shewanella amazonensis SB2B

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate 6937428 Sama_1592 hypothetical protein (RefSeq)

Query= SwissProt::E1V4J5
         (1613 letters)



>FitnessBrowser__SB2B:6937428
          Length = 1613

 Score = 1424 bits (3687), Expect = 0.0
 Identities = 743/1599 (46%), Positives = 1060/1599 (66%), Gaps = 15/1599 (0%)

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

Query: 73   PEAPKVRVLNPDFEEHGWQSTHTFIAVLHEDMPFLVDSVRVELNRRGMTVHAIHNAVLAV 132
                 VRV NP   +HGWQS+HT I V+  DMPFL DS+ + LNR G+T H + +  LA+
Sbjct: 71   VGDTHVRVFNPTQSKHGWQSSHTIIEVIQPDMPFLTDSLGMALNRLGVTTHMMLHTPLAI 130

Query: 133  GRDDEHRLQRVASPEETDAPEARESLIAIEVDRHSNPAELEEIEASLLEVLREVRTAVSD 192
            GR D+  +  V   +++   + + ++  IE+DR S+ A+L+ +   +  VL +V  AV D
Sbjct: 131  GRSDKG-IDSVGFVKDSPESDDKVAIFLIEIDRQSSEADLKNLLGEVQSVLTDVHAAVKD 189

Query: 193  FDPMRAQARAAIEELEATRPAQVDPADHREAIEFLQWLLQDNFTFLGYDEYEVREDQGRQ 252
            +  M  +  A I EL   +P      +  EA+ FL +L   +FT LGY +Y+++  +G  
Sbjct: 190  WQAMSDKLTATITELPK-QPFPGTKEELDEAVAFLTYLNNHHFTLLGYRQYDLKRVEGDM 248

Query: 253  RLDKVQNSELGVFRLDQPRYRER---IRTDLGVEGDHYVPMPQLMSFAKSAHHARIHRPT 309
             L  V N E G+  +++P   +    + + L            L+   KS+  +R+HRP 
Sbjct: 249  EL--VPNLESGLGLMNKPGKHKPDALMLSTLSNSARKEALDHSLLILTKSSTKSRVHRPA 306

Query: 310  YPDYISIDRYDDQGRVIGERRFLGMFTATVYNESPRNVPILRRKLQAVMDIAGFSPKGHN 369
            Y DYI I R+D +G V+GE RF+G++ + +YN SPR +P+L +K+Q V+D +G  P+ H+
Sbjct: 307  YVDYIGIKRFDKKGNVVGEDRFIGLYASNLYNRSPREIPLLAQKVQRVLDNSGLVPRSHD 366

Query: 370  GKQLLQILEVYPRDDLFQIDIEELAQTALGILDIRERRRVRLFIREDTFGKFYSCLVFVP 429
             K L+ ILE  PRD++ Q + +EL+Q A G+L++++R +++LF+R+D FG+F SCLV+V 
Sbjct: 367  YKALVNILENLPRDEIIQANEQELSQVAHGVLEMQDRDKLKLFVRKDGFGRFLSCLVYVS 426

Query: 430  RDVFSTELRVRLQELLCEELDATFG-DFNTYLSESVLARIQFILRFNGEKPVEYDIKRLE 488
            +D ++T+LR   Q +L +   +    +F TY SES LAR  +I++ +    ++ D+  +E
Sbjct: 427  KDRYNTKLRQDTQRILAQHFQSKEEVEFTTYFSESTLARTHYIVKVDNNN-MDVDVAAIE 485

Query: 489  EKLVKLARNWRDDLLNASIEGFGEESANLLMSRFRDAFPASYREDFSARTAVYDLQHIGE 548
              L++ AR+W D L N+     GEE  N L  R+  AF  SY+ED     AV D+Q +  
Sbjct: 486  NNLIEAARSWEDKLYNSLNHAMGEEQGNRLSKRYLTAFSRSYKEDVLPNAAVVDIQQLEA 545

Query: 549  LDEGAPLALSLYRLIEE--EGSGVNLKLFHRGAPIPLSDVLPMMENLGLRVIGERPYEVQ 606
            LDE   L +  Y+  E     + V LKLFH+  PI LSDVLPM+EN GLRVI ERPYEV+
Sbjct: 546  LDEEHKLGMLFYQPQEAALNSNKVRLKLFHKDEPIHLSDVLPMLENFGLRVINERPYEVK 605

Query: 607  ASD-ASYWIHDFNLEHHTSVEMNLQEMRGPFIEAFQRIWAGEADNDAFNRLIIGANLDWR 665
              D A++WI DF +        NL + +  F  A  ++W  + ++D FNRL++   L  R
Sbjct: 606  TPDGATFWILDFLMMVTGGNTENLADSQDRFQTALSQVWNKKLEDDGFNRLVLSTGLAGR 665

Query: 666  EVAMLRAYARYLKQIRFGMSQDYIATTLGSHPEITRELVSLFELRFDPAERPGEGDIEEC 725
            EV++LRAYA+Y++QI    SQ YI  T   +PEI   LV +F  +F+P  +     + + 
Sbjct: 666  EVSILRAYAKYMRQIDATFSQAYIEQTFARYPEIADLLVKMFIRKFNPKLKTRT--LTKF 723

Query: 726  ESRILTLLDEVPSLNDDQLLRRYMELIKATLRTNYYQRTEEGRYKDYLAFKLDPSQVSGI 785
            + ++   L++V SL+DD+++RRY++LI AT+RTN+YQ   +G  KDY++FK  P  +  +
Sbjct: 724  KEQLNLRLEDVASLDDDRIIRRYLDLINATVRTNFYQTKADGENKDYVSFKFIPKMIPEM 783

Query: 786  PKPCPAYEIFVCSPRVEGVHLRGGKVARGGLRWSDRHEDFRTEVLGLVKAQQVKNAVIVP 845
            PKP PA+EIFV SPRVEGVHLRGGKVARGGLRWSDR EDFRTEVLGLVKAQ VKN VIVP
Sbjct: 784  PKPLPAFEIFVYSPRVEGVHLRGGKVARGGLRWSDRREDFRTEVLGLVKAQNVKNTVIVP 843

Query: 846  MGAKGGFVCKRMPEGADREATQKEGIACYQIFIRALLDVTDNLVGGEVVPPRDVVRHDDN 905
            +GAKGGFVCK+ P    REA   EG  CY+IFIR LLDVTDN++ GE+VPP DVVRHD++
Sbjct: 844  VGAKGGFVCKQSPVDGGREAIFTEGQECYRIFIRGLLDVTDNIINGEIVPPVDVVRHDED 903

Query: 906  DPYLVVAADKGTATFSDIANEISTEYGHWLGDAFASGGANGYDHKKMAITAKGAWESVKR 965
            D YLVVAADKGTATFSDIAN IS EY HWLGDAFASGG+NGYDHKKM ITAKG WESVKR
Sbjct: 904  DAYLVVAADKGTATFSDIANAISIEYNHWLGDAFASGGSNGYDHKKMGITAKGGWESVKR 963

Query: 966  HFRGLGVNTQEDEFSVVGIGDMAGDVFGNGMLLSDKIRLVGAFNHLHIFVDPTPDAAASF 1025
            HFR +G++ Q  +F+ +GIGDMAGDVFGNGMLLS+   LV AFNH+HIF+DPTPDAAASF
Sbjct: 964  HFREIGIDCQTTDFTCLGIGDMAGDVFGNGMLLSEHTCLVAAFNHMHIFIDPTPDAAASF 1023

Query: 1026 AERQRLFDMPRSSWEDYNTELISEGGGIFPRSAKSITITPQMKKVFGIREDKLSPNELIR 1085
             ER+RLF++PRSSW+DYN ELIS+GGGIF RSAKSIT++P+MK++ G  +  ++P EL++
Sbjct: 1024 KERERLFNLPRSSWDDYNRELISKGGGIFLRSAKSITLSPEMKQMLGTDKASMNPTELLK 1083

Query: 1086 AMLVSKVDLVWNGGIGTYVKSSEETDAEVGDKANDALRIDGRELNCRVVGEGGNLGLTQR 1145
             +L  +VDL+WNGGIGTYVKSS ET+AEVGD+AND LR++GR++  +++GEGGNLG TQ 
Sbjct: 1084 ELLKMEVDLIWNGGIGTYVKSSRETNAEVGDRANDGLRVNGRDVRAKIIGEGGNLGCTQL 1143

Query: 1146 GRMEAAAKGVRVNTDFIDNAGGVNCSDHEVNIKILIDEVVSRGDLTEKQRNQLLADMTDE 1205
            GR+E A  G R+NTDF+DN GGV+CSD+EVNIKIL++ +V+ G++T KQRN+LL +MTDE
Sbjct: 1144 GRIEYAMNGGRMNTDFVDNVGGVDCSDNEVNIKILLNAMVAEGEMTLKQRNRLLEEMTDE 1203

Query: 1206 VSELVLLDNYRQTQALDLAELLSRQGIGPYRRFISELEAAGQIDRELEFLPSDEELLERT 1265
            VSE+VL D   QT+ + + ++   + +    RFI  LE  G++DR LEFLP+D+EL ER 
Sbjct: 1204 VSEIVLQDCKDQTRTISVTQVRGAEQLKEQIRFIHYLEKEGKLDRALEFLPTDDELAERL 1263

Query: 1266 QHNQGMTLPELSVLISYAKSVLKGDLIASDVPDDPTIMRFVERVFPSMLAERYRDEMYEH 1325
               + +T PELSVL++YAK VLK  L+  ++ +D  + + +   FP  L E Y D+M  H
Sbjct: 1264 AAGKPLTRPELSVLVAYAKMVLKEQLLKPEITEDSFLSKLLVSYFPQKLQELYADKMNTH 1323

Query: 1326 RLKREIVATQVANDLVDYMGVVFVRRLMDSTGADRADIARAYVIARDSFQLPRLWEQIEA 1385
             L+ EI+AT +AN+LV+ MG+ FV+R+ D TGA  A++A  Y +AR+ F L  L + I A
Sbjct: 1324 PLRGEIIATSLANELVNDMGLNFVQRMQDETGATVAEVAICYTMAREVFGLAELTKAITA 1383

Query: 1386 LDNKVPSQVQYSMMLDLMRMLRRSTRWFLRQRT-GMSTRDTIDYFAPRLAQLQENIGKRL 1444
             +  VP+ VQ  M+  L R +RR+ RWFLR R   +    T+ ++ P   +L+ N+ K +
Sbjct: 1384 QNVVVPAVVQMEMLHQLRRNVRRACRWFLRHRNRTVGIEQTVAFYKPVFEELKANVNKYM 1443

Query: 1445 RGEEQEQWSARRQELVKAGVPEALASTVAAAGSLYAALGIIQTARQTDEKPQRVAEIFYE 1504
              EE +  +A    L K  V   +A+ +A   +L++AL I Q A+  ++    VAE +++
Sbjct: 1444 VAEEVDAITAEIHALEKEQVSSDVANVIANMSTLFSALDIAQIAQNENKPVALVAETYFK 1503

Query: 1505 VGARLELPWIIQQVTRLEVRDGWQAKARDTFRDDIDRQQLALTASVLGMDGGPRDSAERV 1564
            +GA++EL W ++Q++   V + WQA AR  FR+++D QQ AL+++VL        +   +
Sbjct: 1504 LGAKVELHWFLEQISAQPVANHWQALARAAFREELDWQQRALSSAVLRTCTDTCSADAII 1563

Query: 1565 DRWLSLHEGMHQRWRHLLEEVGSGSQGGFPLFAVAVREL 1603
            + W+  +  + +RW H+L +  +     F  F+VA+REL
Sbjct: 1564 EGWIEANRVLLERWFHMLADFKTTQSHEFAKFSVALREL 1602


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: 5533
Number of extensions: 261
Number of successful extensions: 12
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: 1613
Length adjustment: 51
Effective length of query: 1562
Effective length of database: 1562
Effective search space:  2439844
Effective search space used:  2439844
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.

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