Alignments for a candidate for gdhA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Marinobacter adhaerens HP15

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate GFF2745 HP15_2689 NAD-specific glutamate dehydrogenase

Query= BRENDA::A0A0H3C571
         (1607 letters)



>FitnessBrowser__Marino:GFF2745
          Length = 1128

 Score =  861 bits (2224), Expect = 0.0
 Identities = 481/1143 (42%), Positives = 692/1143 (60%), Gaps = 20/1143 (1%)

Query: 468  ARIADTALTWEDRFEA-VVRAGGAPTGGVRTLLDKYGYAFPPGYRDQYDALEALADIDII 526
            AR+ + + +W+D     +VR+ G   GG       +   FP  YR ++   EALADI  I
Sbjct: 2    ARMVEESRSWDDDLHGELVRSFGESIGG--RYAQVFSGGFPSAYRARFPVSEALADIGQI 59

Query: 527  ETLTEGALPRVRAFRRFEDGPRTFRFKLYLRGAAAPLAEVLPILERMGLKALIEDGFRLS 586
            +++       +R ++  +     F FKLY  G    L++V+PILE +G++ L E  +R  
Sbjct: 60   QSIAVSTDVPMRFYQPRDPSETGFHFKLYSEGQPVILSDVIPILENLGMRVLGEHPYR-- 117

Query: 587  IHEKDGPHSVWVHEFVLD-DPAGEHIVFDEVRQVFEEAFIAIWTGATENDGFNRIVLEMA 645
            +  +DG  +  V +F ++             R + + AF  IW G  END FN++++   
Sbjct: 118  VRRRDG-ENFGVSDFTVELHDRCRQADLSAARPLIQSAFREIWNGFAENDDFNQLIMLCG 176

Query: 646  VGWREAALLRALARYRQQSGLDPSQQVQEAALRDHPMVARLILDLFRVKFDPAIRADLRT 705
            + WRE AL+RA ARY +Q     SQ      L  HP +   ++  F  +F+P ++     
Sbjct: 177  LNWREVALIRAYARYVKQLRFGFSQPFIAETLARHPDITSRLVAFFFNRFEPGVKG---- 232

Query: 706  RREQAEAVQFSIVEALQAVESLDADRVLRRLAALVGAIQRTNFYQLGADGEPKSYISFKI 765
            R+ + E ++  + ++L+AV SLD DR+LRR   L+ A  RTN++Q+  DG   SY+S K+
Sbjct: 233  RKSRTEKLEAELRDSLEAVASLDDDRILRRFFMLIRATLRTNYFQVREDGGFPSYLSLKL 292

Query: 766  ASRELEDLPAPKPYREIYVSAPHVEGVHLRFGPVARGGLRWSDRRDDFRTEVLGLVKAQQ 825
                + D+P P+P  EI+V +P +EGVHLR GPVARGGLRWSDR +D+RTE+LGLVKAQQ
Sbjct: 293  DPSSIPDIPRPRPKFEIFVYSPRIEGVHLRAGPVARGGLRWSDRIEDYRTEILGLVKAQQ 352

Query: 826  VKNAVIVPVGSKGGFYPKQLPRGGDRDAIQAEAIRAYKTFLSGLLDLTDNIDSDNQVVPP 885
            VKN+VIVP G+KGGF  KQ PR G R+A++ E +  Y+TF+ GLLD+TDN+D D QVVPP
Sbjct: 353  VKNSVIVPAGAKGGFVVKQPPRDGSREAVREEGVACYQTFIRGLLDITDNLD-DGQVVPP 411

Query: 886  PSVIAHDAQDPYLVVAADKGTATFSDIANGVAESYGFWLGDAFASGGSVGYDHKVMGITA 945
             +V+ +D+ D YLVVAADKGTATFSDIAN +A  Y FWLGDAFASGGS GYDHK MGITA
Sbjct: 412  ANVVRYDSDDTYLVVAADKGTATFSDIANALAAEYNFWLGDAFASGGSEGYDHKKMGITA 471

Query: 946  RGAWEAVKRHFRELGKDIQTEAFTVVGVGDMSGDVFGNGMLLSKQTKLLAAFDHRHIFLD 1005
            RGAWE+VKRHF E G D Q++ FTVVG+GDM GDVFGNGMLLS Q +L+ AF+H+HIF+D
Sbjct: 472  RGAWESVKRHFLEKGTDTQSDEFTVVGIGDMGGDVFGNGMLLSDQIRLIGAFNHQHIFVD 531

Query: 1006 PNPDPAVSWAERDRMFKLPRSSWEDYDKSKISAGGGVFARSLKSIPLSAEVRAMLEIKAE 1065
            P+PD A S+ ER+R+FKL  SSW DYD   IS GGGVF+RS+KSIP+S+++R +L IKA 
Sbjct: 532  PDPDAAASFRERERLFKLSGSSWADYDTQLISDGGGVFSRSMKSIPVSSQMRKVLGIKAR 591

Query: 1066 AVSPAELMTAILKSKAELLYLGGIGTYVKAKGETNADAGDKANDAIRINGSDLRVKVVGE 1125
            ++SPA+L++A+LK+  ++L+ GGIGTYVKA  E++ D GDK NDA+RI+ ++LR K +GE
Sbjct: 592  SLSPADLISALLKAPVDMLWNGGIGTYVKAPSESHEDVGDKTNDALRIDSNELRCKALGE 651

Query: 1126 GANLGLTQAGRIEFAQAGGHINTDAIDNSAGVDSSDHEVNIKILTGILERGGQLDRESRN 1185
            G NLG+TQ  RI+FA+ GG +N+D IDN+ GVD SDHEVNIKIL   L     +    RN
Sbjct: 652  GGNLGVTQKARIDFARRGGSVNSDFIDNAGGVDCSDHEVNIKILLNDLVHRQLMSLPERN 711

Query: 1186 TLLASMTDDVAHHVLEHNYDQTLALTLLESDAVSEVDAQIRYMVNLEQRGRLDRRVEGLP 1245
             +L +MT +VA  VL +NY Q +AL+L ++ AV+  D   R M  LE  G+LDR +E LP
Sbjct: 712  RMLRAMTSEVAELVLRNNYRQAMALSLAQNPAVATADQYERLMRRLETEGKLDRSLEFLP 771

Query: 1246 TNTTLLERKAAGRGLTRPELAVLLAYGKLDLFDEIVASQSPDDPWFERTLRGYFPRA-LD 1304
            ++  L  R+  G GLTRPELAVL++Y K++L   +VAS    DP F   L   FP + L 
Sbjct: 772  SDEELQARREHGGGLTRPELAVLVSYAKIELKQALVASPIVHDPRFNSALHSAFPASLLA 831

Query: 1305 QYADAMQKHRLKREIIATVVGNQMVNMCGPTFVSRLKAAAGADVNAVVVGFTAAREILGI 1364
             + +A+  H L+ EI AT + N MVN  G T+  R+++A GAD   +   +  +  I  +
Sbjct: 832  AFPEAVGAHPLRAEISATQIANDMVNRMGITWFDRIRSATGADAGRIASAYLISLRIHDV 891

Query: 1365 DGLWDQVNGLDNKASAEGQTALYKALAYALRSLTFWLARRAQRDAANVQTLVEAYGPSVA 1424
            D  W+ +  LD K  A  Q  L+      +   T WL +  +R A +  + ++ Y   ++
Sbjct: 892  DAHWESMELLDGKIDAGVQADLFADAIRLVTRSTSWLLQN-RRQALDPVSCIDHYRAPMS 950

Query: 1425 ALKALAPAILSPFEQKAVSKRVKAYVADGAPEALALSVAALQPLTTAADLVDLANASSWS 1484
             + A    + S        +R   Y     PE L+   A+ +      D+V++A      
Sbjct: 951  DVLASKSRLESVIPASRWYERYAEYCERMVPEDLSAWCASAESRYWLMDMVEIARQLDEK 1010

Query: 1485 VENVARLYHQVGAAFGFDRLRGAAGSFVGGDAFERLAVRRLIEDMLTEQTSITQQVLKFA 1544
            +E+VA +Y  +G +     L     +F     ++ LA     +++  +  ++T  V    
Sbjct: 1011 LESVAWVYFTLGESLNLTWLDRQMRAFRANGHWQVLATIHFRDELDHQLRNLTLSVF--- 1067

Query: 1545 ANAQAGEDEAAAKAAISSWAALRGDRPRAVKRTIEDIEQAGGGWTFAKLTIANAALRELS 1604
              ++  + +   +  I +W   +       +R + D+ QA      A  ++A+  LREL+
Sbjct: 1068 --SEPVDGDGTPEKRIEAWRGNKRMLLARWERMLNDM-QAANDVDCAVFSVAHGVLRELA 1124

Query: 1605 SAA 1607
              A
Sbjct: 1125 LKA 1127


Lambda     K      H
   0.319    0.135    0.390 

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: 3896
Number of extensions: 177
Number of successful extensions: 6
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: 1607
Length of database: 1128
Length adjustment: 49
Effective length of query: 1558
Effective length of database: 1079
Effective search space:  1681082
Effective search space used:  1681082
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: 59 (27.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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