Alignments for a candidate for gdhA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Magnetospirillum magneticum AMB-1

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate WP_011382479.1 AMB_RS00165 NAD-glutamate dehydrogenase

Query= uniprot:G8AE86
         (1618 letters)



>NCBI__GCF_000009985.1:WP_011382479.1
          Length = 1603

 Score = 1695 bits (4389), Expect = 0.0
 Identities = 890/1613 (55%), Positives = 1125/1613 (69%), Gaps = 29/1613 (1%)

Query: 11   ELTEEVVRQVRERLGRSRAAPAERFVRQFYDNVPPDDIIQAPAEQLYGAALAMWQWGQQR 70
            E++  + R++ E         A R +R +   +P  D+ +A  E +YGAAL ++ + + R
Sbjct: 2    EISAYLDRRIAELSEPLAKVGAGRLIRAYAAGIPLADLAEADPELVYGAALGLFAFLRDR 61

Query: 71   EATDRAKVRVYNPRVEEHGWQSHRTVVEIVNDDMPFLVDSVTAELNRQGLTVHLVIHPVV 130
            +      +RV++P ++ HGW S  +VVEI+NDDMPFLVDSV  EL R+G+ VHL++HPV+
Sbjct: 62   QP-GAPSIRVFDPDLDRHGWVSSHSVVEIINDDMPFLVDSVAMELARRGIKVHLLVHPVL 120

Query: 131  RVKRDADGQLAELYEPAAAPTDAAPESFMHVEVGAVTGAAALDQAREGLERVLADVRAAV 190
            RV RD  G L ++   AA  + + PES MHVE+     A    Q  E L  VLA VR AV
Sbjct: 121  RVDRDGAGTLVQV---AANGSGSTPESVMHVEIDRQP-AEVQTQLAESLAEVLAQVRLAV 176

Query: 191  ADWRAMRQQVRAAIVEADCARAAVPAIIPDDEVDEAKAFLSWADDDHFTFLGYREYRFES 250
            ADWR M + + A + E + A A VPA    DE  EA AFL W  D+HFTFLGYR +    
Sbjct: 177  ADWRRMLETLWAGVTEFENASAKVPA----DEKQEALAFLEWLADNHFTFLGYRRF---- 228

Query: 251  GADGADSSLGLVA--GSGLGILRDDSVTVFDGLRNYATLPPDVRDFLRNPRVLMVTKGNR 308
                 D + G+VA   SGLGIL D    VFD     A +P ++R F++ P  LMVTK  R
Sbjct: 229  -----DLAKGVVADPASGLGILSDAGAHVFDDTVTLADMPAELRAFVQRPDPLMVTKSAR 283

Query: 309  PSPVHRAVPMDAFLIKRFDAEGRIIGERLVAGLFTSVAYNRSPREIPYLRRKVAEVMELA 368
             + +HR V MD   +K+FDA+G+++G     GLFTS AYN  P +IP LRRK+A V   A
Sbjct: 284  HAVIHRPVRMDIIGLKQFDAKGKVVGLHAFLGLFTSAAYNDRPAQIPLLRRKIARVEARA 343

Query: 369  GFDPQGHDGKALLHILETYPRDELFQIQVPELLDIAVGILHLQERQRLALFVRKDPFERF 428
             F+  GHD KAL++ILETYPRDELFQ+    L +I++GILHLQ+RQR+A+F+R D FERF
Sbjct: 344  DFNKSGHDAKALINILETYPRDELFQVSEDALFEISIGILHLQDRQRVAVFLRNDEFERF 403

Query: 429  ASCLVYVPRDRYDTTLRRRIQSILEAAYDGTCTGFTTQLTESVLARLHFIIRTEPGRVPT 488
             SCLV+VPRDRYDT LR  + ++LE A  GT   F TQ+ +  LARLHFIIRT PG +  
Sbjct: 404  VSCLVFVPRDRYDTPLRLAVTAMLEEALGGTLDTFYTQVADLPLARLHFIIRTTPGHLRR 463

Query: 489  VDATDLEARLVQASRGWDDHLRDALVEAHGEEQGRTLFRRYADAFPTAYREEFNAEAAVF 548
            VDA  LE R+  A+R W +HL+DAL++ HGE  G  L RR+   FP +YRE   A AAV 
Sbjct: 464  VDALALEVRIADAARTWHEHLQDALIQTHGEAAGLALARRWGKGFPASYRESHGALAAVA 523

Query: 549  DIERIEKATAQGTLGINLYRPLEAEGDELHVKIYHEGRPVPLSDVLPMLEHMDLKVITEA 608
            D+ RI+ A+  G + +NLYRP+EAE  +  +K+Y  G+PVPLS +LPMLE M L VI E 
Sbjct: 524  DVGRIQTASG-GDIVLNLYRPVEAEPRQGRLKLYRSGQPVPLSGILPMLEAMGLVVIAEV 582

Query: 609  PFEIAIAGHAAPVWIHDFTARSQNGLPIDCAMVKEKFQDAFAAVWDGRMEDDGFNRLVLR 668
            P EI      + VWIHDF   S +G P+D A  +E F DA AAVW G  + DGFNRLVL 
Sbjct: 583  PHEIEPDSGGSTVWIHDFEVESADGAPLDVAERRELFHDALAAVWRGDADSDGFNRLVLS 642

Query: 669  AGLTAREVTVLRAYAKYLRQARIPYGQDVVESTLAGHPAIARKLVALFHSRFDPARRSQN 728
            AGL+ RE+ VLRAY KYLRQ  I Y Q  +E  L G+  +A  LV LF + FDP  RS +
Sbjct: 643  AGLSWREIMVLRAYTKYLRQTGITYSQTYIEQALGGNADMATGLVRLFLASFDPKGRSGD 702

Query: 729  DPGLAAEIERALDGVKNLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYLSFKIDSRN 788
                 A +   LD V + D+DRILRRFLNL+ +TLRTN +Q    G+PK YLSFK+DSR 
Sbjct: 703  ASEAEAALLAGLDKVVSADDDRILRRFLNLIRSTLRTNYFQTDGAGKPKAYLSFKLDSRQ 762

Query: 789  IDDLPLPRPMVEVFVYSPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKNT 848
            +DDLP PRP+VEVFVYSPR+E +HLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKN 
Sbjct: 763  VDDLPAPRPLVEVFVYSPRVEAIHLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKNA 822

Query: 849  VIVPVGSKGGFVVKRPPPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQGAVVPPPEV 908
            VIVPVG+KGGFVVK+PP  + GREA +AEGIECYKTLMRGLLD+TDNL  +G V PPP+V
Sbjct: 823  VIVPVGAKGGFVVKKPPA-AGGREAYMAEGIECYKTLMRGLLDLTDNLVPEG-VRPPPDV 880

Query: 909  VRHDGDDPYLVVAADKGTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKKMGITARGA 968
            +R DGDDPYLVVAADKGTATFSDIAN+VS+++G WLGDAFASGGS GYDHKKMGITA+GA
Sbjct: 881  LRRDGDDPYLVVAADKGTATFSDIANAVSLEYGHWLGDAFASGGSQGYDHKKMGITAKGA 940

Query: 969  WESVKRHFRELGHDTQTQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHRHIFIDPDP 1028
            W +V+RHFRE+G DT+++DFTV+GVGDMSGDVFGNG+L S H +L+AAF+H HIF+DPDP
Sbjct: 941  WVAVERHFREMGIDTRSEDFTVIGVGDMSGDVFGNGLLRSPHAKLVAAFNHAHIFLDPDP 1000

Query: 1029 DAARSWEERQRLFDLPRSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRFGIAKDHVT 1088
            D  +++ ER+RLF+  ++ W DYD S +S GG ++ RSAKS+ ++P+ + RFGI  + +T
Sbjct: 1001 DPQKTFTERERLFNAVKA-WPDYDLSTISPGGGIWPRSAKSIPISPQAKARFGIEANSLT 1059

Query: 1089 PLELMQTLLKAEVDLLWFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRAKVIGEGAN 1148
            P EL++TLLKA VDLL+ GGIGTY+KA+ E+NA+ GD+AND LR++G +V A+V+GEGAN
Sbjct: 1060 PTELIRTLLKAPVDLLFLGGIGTYVKASGESNADAGDRANDTLRVNGSEVGARVVGEGAN 1119

Query: 1149 LGVTQRGRIEAAQHGV-----RLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMTLKQ 1203
            LG TQ GRIE A  G      R++TDAIDNSAGVD SDHEVNIKIL+ND+V  GD+T KQ
Sbjct: 1120 LGFTQLGRIEYAISGAGGGGGRIDTDAIDNSAGVDCSDHEVNIKILVNDLVAAGDLTPKQ 1179

Query: 1204 RDQLLAAMTDEVAGLVLADNYLQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRAIEY 1263
            RD+LLA MT EV  LVL DNYLQ+QA+++  AQG D L+A+AR +R LEK GRL+RAIE+
Sbjct: 1180 RDKLLAEMTGEVGALVLRDNYLQTQAISMLEAQGADLLDAEARFMRLLEKGGRLDRAIEF 1239

Query: 1264 LPDEEELSARMANREGLTRPELAVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFPKPL 1323
            LP +E L+ R A ++G TRPELAVLLAY KI LYD +LAS+LPDDPFMA DLT YFP  L
Sbjct: 1240 LPTDETLTERAARKQGFTRPELAVLLAYGKIWLYDHILASELPDDPFMAIDLTNYFPTQL 1299

Query: 1324 RKAHAEAVGRHRLRREIIATSVTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVRDAF 1383
            R      + RHRLRREI+AT VTNS+VNR G  FV E+ME TG  PA VARAY + RDAF
Sbjct: 1300 RDRFGHEIQRHRLRREIVATVVTNSIVNRVGGAFVSELMETTGHPPAQVARAYIVARDAF 1359

Query: 1384 GLRSLWTGIEDLDTVVPAALQTSMILETVRHMERAAAWFLASCQQPLDIARETEAFRPGI 1443
             +R +W  IE+LD  VPAA QT+M  E  R +ERA  W L S   P  +        PG+
Sbjct: 1360 RMREVWRAIEELDGKVPAAAQTAMQNEANRLVERATLWVLRSMPSPFALGAGISELSPGV 1419

Query: 1444 ETLLAGLDNVLDAEETARLTARVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGRTGR 1503
            + L   +  +L  +  A + AR+  +  QGVP +LA+R+  L VLA+A D++RIA R   
Sbjct: 1420 KALEGAVPAILPPDAAAAVLARIDHFVGQGVPHDLAQRVGNLIVLASAADILRIATRQNL 1479

Query: 1504 GVADVAAVYFMLGRRFGLEWLRDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRVLEA 1563
             +     +YF +G RF L WLR  A       HW K A AA ++DL+ HQ  +T+ V  +
Sbjct: 1480 SIETAGRLYFAVGARFSLGWLRASAEKLSGRGHWLKLAAAAAIEDLYGHQRDITSVVAAS 1539

Query: 1564 VDQLPAEAPVEAWIAHRRPVVERVEQLLSELRTQPNVDLSMLAVANRQLRGLT 1616
               L  +A V+AW+   R  VER E LL+EL+   ++DLSM+ VANRQLR LT
Sbjct: 1540 YPDLEPDAAVQAWLEANRAAVERAETLLAELKAASHIDLSMIMVANRQLRTLT 1592


Lambda     K      H
   0.320    0.136    0.399 

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: 6033
Number of extensions: 277
Number of successful extensions: 14
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: 1618
Length of database: 1603
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1552
Effective search space:  2431984
Effective search space used:  2431984
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
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