Alignments for a candidate for gdhA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Halomonas desiderata SP1

Align NAD-specific glutamate dehydrogenase; NAD-GDH; NAD(+)-dependent glutamate dehydrogenase; EC 1.4.1.2 (characterized)
to candidate WP_086510832.1 BZY95_RS15665 NAD-glutamate dehydrogenase

Query= SwissProt::E1V4J5
         (1613 letters)



>NCBI__GCF_002151265.1:WP_086510832.1
          Length = 1613

 Score = 2545 bits (6597), Expect = 0.0
 Identities = 1245/1607 (77%), Positives = 1423/1607 (88%), Gaps = 2/1607 (0%)

Query: 7    EEARLDLLKQLKERLQSRLDKDKAAEVDTFAHLFYAAVPLEDLADRRLDDLYGATLSVWH 66
            E  R ++LKQL+ERL SRL+K +A EV+ FA  FYA VPLEDLADRRLDDLYGATLSVWH
Sbjct: 7    EVGRQEILKQLRERLDSRLEKARAEEVEAFARHFYATVPLEDLADRRLDDLYGATLSVWH 66

Query: 67   FIQQFDPEAPKVRVLNPDFEEHGWQSTHTFIAVLHEDMPFLVDSVRVELNRRGMTVHAIH 126
            +IQ FD  +PKVRV NPDFEEHGWQS+HTF+AVLHEDMPFLVDSVR+ELNRR +TVHAIH
Sbjct: 67   YIQHFDHASPKVRVFNPDFEEHGWQSSHTFVAVLHEDMPFLVDSVRIELNRRALTVHAIH 126

Query: 127  NAVLAVGRDDEHRLQRVASPEETDAPEARESLIAIEVDRHSNPAELEEIEASLLEVLREV 186
            NAVLAV R+  H L RV SP + DAPE RESLIAIE+DRHSNP  L +IE SL EVLR+V
Sbjct: 127  NAVLAVERNSSHDLVRVGSPRDADAPEQRESLIAIEIDRHSNPEVLADIEQSLHEVLRDV 186

Query: 187  RTAVSDFDPMRAQARAAIEELEATRPAQVDPADHREAIEFLQWLLQDNFTFLGYDEYEVR 246
            R AV D+D M  +A  A+ EL+A RP Q++P DH EAI FL+WL++DNFTFLGYD + + 
Sbjct: 187  RIAVGDYDAMHERALEAVAELKAGRPEQIEPGDHEEAIAFLEWLVRDNFTFLGYDAFAIE 246

Query: 247  EDQGRQRLDKVQNSELGVFRLDQPRYRERIRTDLGVEGDHYVPMPQLMSFAKSAHHARIH 306
             D    RL K Q SELGVFRLD PRY+ERIRT+LG+E + +V +PQL+SFAKS+HHAR+H
Sbjct: 247  SDADGDRLVKEQGSELGVFRLDLPRYQERIRTELGIENNRFVLVPQLLSFAKSSHHARVH 306

Query: 307  RPTYPDYISIDRYDDQGRVIGERRFLGMFTATVYNESPRNVPILRRKLQAVMDIAGFSPK 366
            RPTYPDY+SIDRYD+QGRVIGE RFLG+FTA+VYNESPRN+P+LRRKL+AVM+IAGF+PK
Sbjct: 307  RPTYPDYVSIDRYDEQGRVIGEHRFLGLFTASVYNESPRNIPLLRRKLKAVMEIAGFNPK 366

Query: 367  GHNGKQLLQILEVYPRDDLFQIDIEELAQTALGILDIRERRRVRLFIREDTFGKFYSCLV 426
            GHNGKQLLQILEVYPRDDLFQID +ELA TALGILDIRERRRVRLFIR D  G+F+SCLV
Sbjct: 367  GHNGKQLLQILEVYPRDDLFQIDTQELAHTALGILDIRERRRVRLFIRTDRSGRFHSCLV 426

Query: 427  FVPRDVFSTELRVRLQELLCEELDATFGDFNTYLSESVLARIQFILRFNGEKPVEYDIKR 486
            FVPRDVFST+LRVR+Q LLCEELDATFGDFNTYLSES+LARIQFILRF G+ P E ++KR
Sbjct: 427  FVPRDVFSTDLRVRIQNLLCEELDATFGDFNTYLSESILARIQFILRFRGDVPREVNLKR 486

Query: 487  LEEKLVKLARNWRDDLLNASIEGFGEESANLLMSRFRDAFPASYREDFSARTAVYDLQHI 546
            LE K+ +LAR+WRD+L  A +EGFGEE AN LM RFRDAFPASYR+DF +RTAV+DLQH+
Sbjct: 487  LEAKVAQLARSWRDELHEALVEGFGEEQANRLMDRFRDAFPASYRDDFGSRTAVFDLQHL 546

Query: 547  GELDEGAPLALSLYRLIEEEGSGVNLKLFHRGAPIPLSDVLPMMENLGLRVIGERPYEVQ 606
             +LD G PLAL+LYRL+EEEGSGVNLKLF R   IPLSDVLP+MENLGLRVIGERPYE+ 
Sbjct: 547  ADLDAGEPLALTLYRLVEEEGSGVNLKLFQRDRTIPLSDVLPVMENLGLRVIGERPYEIV 606

Query: 607  ASDASYWIHDFNLEHHTSVEMNLQEMRGPFIEAFQRIWAGEADNDAFNRLIIGANLDWRE 666
              D  YW+HDF+LEHHTS E++LQ+MR PFIEAF+RIW GEA+ND FNRL+I ANLDWRE
Sbjct: 607  TPDVRYWLHDFDLEHHTSTEVSLQKMREPFIEAFKRIWVGEAENDGFNRLVIAANLDWRE 666

Query: 667  VAMLRAYARYLKQIRFGMSQDYIATTLGSHPEITRELVSLFELRFDPAERPGEGDIEECE 726
            VAMLRAYARYLKQIRFGMSQDYIA+ L ++PEITRELV+LF+LRFDPA+RPGE ++E C 
Sbjct: 667  VAMLRAYARYLKQIRFGMSQDYIASALTNYPEITRELVALFKLRFDPADRPGEEEVEACV 726

Query: 727  SRILTLLDEVPSLNDDQLLRRYMELIKATLRTNYYQRTEEGRYKDYLAFKLDPSQVSGIP 786
             RI   LD V SLNDDQLLRR+ME+I+ATLRTNYYQR+  G +KDY+A+KLDP++++G+P
Sbjct: 727  ERINRHLDGVASLNDDQLLRRFMEMIQATLRTNYYQRSAGGGFKDYIAYKLDPTRITGMP 786

Query: 787  KPCPAYEIFVCSPRVEGVHLRGGKVARGGLRWSDRHEDFRTEVLGLVKAQQVKNAVIVPM 846
            KP PA+EIFVCSPRVEGVHLRGGKVARGGLRWSDRHEDFRTEVLGLVKAQQVKNAVIVP+
Sbjct: 787  KPRPAFEIFVCSPRVEGVHLRGGKVARGGLRWSDRHEDFRTEVLGLVKAQQVKNAVIVPV 846

Query: 847  GAKGGFVCKRMPEGADREATQKEGIACYQIFIRALLDVTDNLVGGEVVPPRDVVRHDDND 906
            GAKGGFVCKR+PEG DR+A Q+EGIACY+ FIRALLDVTDNLVGGEVVPPRDVVRHDD+D
Sbjct: 847  GAKGGFVCKRLPEGGDRDAIQQEGIACYKTFIRALLDVTDNLVGGEVVPPRDVVRHDDDD 906

Query: 907  PYLVVAADKGTATFSDIANEISTEYGHWLGDAFASGGANGYDHKKMAITAKGAWESVKRH 966
             YLVVAADKGTATFSDIANEIS EYGHWLGDAFASGGANGYDHKKM ITA+GAWESVKRH
Sbjct: 907  AYLVVAADKGTATFSDIANEISVEYGHWLGDAFASGGANGYDHKKMGITARGAWESVKRH 966

Query: 967  FRGLGVNTQEDEFSVVGIGDMAGDVFGNGMLLSDKIRLVGAFNHLHIFVDPTPDAAASFA 1026
            FR LG+NTQE+EF+VVGIGDM GDVFGNGMLLSDKIRLVGAFNHLHIFVDP PDAAA+FA
Sbjct: 967  FRNLGLNTQEEEFTVVGIGDMGGDVFGNGMLLSDKIRLVGAFNHLHIFVDPNPDAAATFA 1026

Query: 1027 ERQRLFDMPRSSWEDYNTELISEGGGIFPRSAKSITITPQMKKVFGIREDKLSPNELIRA 1086
            ER+RLF++PRSSWED++  LISEGGG+F RSAKSI +TPQMK+VFGI ED+LSPN+ IRA
Sbjct: 1027 ERKRLFELPRSSWEDFDASLISEGGGVFKRSAKSIAVTPQMKEVFGIAEDRLSPNDFIRA 1086

Query: 1087 MLVSKVDLVWNGGIGTYVKSSEETDAEVGDKANDALRIDGRELNCRVVGEGGNLGLTQRG 1146
            ML S++DL+WNGGIGTYVK S ETDA VGDKANDALRI+G ELNCRVVGEGGNLGLTQRG
Sbjct: 1087 MLKSQIDLLWNGGIGTYVKGSAETDAMVGDKANDALRINGGELNCRVVGEGGNLGLTQRG 1146

Query: 1147 RMEAAAKGVRVNTDFIDNAGGVNCSDHEVNIKILIDEVVSRGDLTEKQRNQLLADMTDEV 1206
            RMEAAAKGV VNTDFIDNAGGVNCSDHEVNIKILIDEVV RGD+T+KQRNQLLADMT+EV
Sbjct: 1147 RMEAAAKGVLVNTDFIDNAGGVNCSDHEVNIKILIDEVVKRGDMTDKQRNQLLADMTEEV 1206

Query: 1207 SELVLLDNYRQTQALDLAELLSRQGIGPYRRFISELEAAGQIDRELEFLPSDEELLERTQ 1266
            ++LV+LDNYRQTQALD++ + SRQGI PYRRFIS LEAAGQ+DRELEFLPSDEELLER  
Sbjct: 1207 ADLVILDNYRQTQALDISAIFSRQGIDPYRRFISGLEAAGQLDRELEFLPSDEELLERAN 1266

Query: 1267 HNQGMTLPELSVLISYAKSVLKGDLIASDVPDDPTIMRFVERVFPSMLAERYRDEMYEHR 1326
              QGMT PELSVLISY+KSVLKG+++ASDVPDDP I ++VER+FP +L ER+ DEMY+HR
Sbjct: 1267 SEQGMTHPELSVLISYSKSVLKGEVLASDVPDDPYIQQYVERIFPRVLVERFPDEMYDHR 1326

Query: 1327 LKREIVATQVANDLVDYMGVVFVRRLMDSTGADRADIARAYVIARDSFQLPRLWEQIEAL 1386
            LKREIV+TQVANDLVD+MG+VFVR L+DSTGA  ADIARAYVIARDSFQL  LWE+IEAL
Sbjct: 1327 LKREIVSTQVANDLVDHMGIVFVRLLIDSTGASPADIARAYVIARDSFQLSSLWERIEAL 1386

Query: 1387 DNKVPSQVQYSMMLDLMRMLRRSTRWFLRQRTGMSTRDTIDYFAPRLAQLQENIGKRLRG 1446
            DN+VPSQVQY+MM DL+R++RR+TRWFLRQR G+STRD I+YFAPR+AQLQE+IG+ LRG
Sbjct: 1387 DNQVPSQVQYNMMTDLIRLIRRTTRWFLRQRLGLSTRDAIEYFAPRVAQLQESIGELLRG 1446

Query: 1447 EEQEQWSARRQELVKAGVPEALASTVAAAGSLYAALGIIQTARQTDEKPQRVAEIFYEVG 1506
            EE+E+W  +R EL++AGVPE LA+TVAA+GSLY ALGIIQ ARQ DEKPQRVAE+F+E+G
Sbjct: 1447 EERERWEHKRGELLEAGVPEELAATVAASGSLYGALGIIQAARQADEKPQRVAEVFFEIG 1506

Query: 1507 ARLELPWIIQQVTRLEVRDGWQAKARDTFRDDIDRQQLALTASVLGMDGGPRDSAERVDR 1566
             RLELPW+IQQV+ L VRD WQA+AR+TFRDDIDRQQLALT SVL  D G R+  ERVD 
Sbjct: 1507 NRLELPWMIQQVSNLNVRDSWQAQARETFRDDIDRQQLALTVSVLKTDDG-REPDERVDN 1565

Query: 1567 WLSLHEGMHQRWRHLLEEV-GSGSQGGFPLFAVAVRELVDLAESNSE 1612
            WL+ H  +H+RW  L+ EV G GSQ  FPLFAVAVRELVDLAESN E
Sbjct: 1566 WLATHASLHERWCRLIAEVRGGGSQSSFPLFAVAVRELVDLAESNGE 1612


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: 6735
Number of extensions: 296
Number of successful extensions: 3
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 24 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