GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Nocardioides daejeonensis MJ31

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_110208307.1 DNK54_RS17595 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_003194585.1:WP_110208307.1
          Length = 492

 Score =  409 bits (1052), Expect = e-119
 Identities = 222/484 (45%), Positives = 305/484 (63%), Gaps = 11/484 (2%)

Query: 18  IENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSL 77
           ++ +LFI GE+  AA+  TFET+DP     LA +A  ++ D+DRA++AA   F    WS 
Sbjct: 1   MQQKLFIGGEFVDAADGGTFETIDPHDGTVLANVAEARAADVDRAVAAAASAFPA--WSR 58

Query: 78  SSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDK 137
            + A R  +L +LAD +E   + LALLET DTG P+R +   D+P  A   R++    DK
Sbjct: 59  MAAADRGRLLLRLADAIEDDVDALALLETRDTGHPVRDTRGLDVPRTAATFRYFGGMADK 118

Query: 138 VYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSP 197
             G V       L  +V EP+GV+  IVPWNFP++ T WK+GPALAAGN V++KPSE SP
Sbjct: 119 FQGSVVPVEQGFLDYVVPEPLGVVGQIVPWNFPVMFTSWKMGPALAAGNCVVMKPSEISP 178

Query: 198 LSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAG 257
           LSA+R+A LA E G P GV+N+V GFG  AG  +  H  I  I+FTGST  G+ + + A 
Sbjct: 179 LSALRVAELAAEVGFPPGVINMVPGFGATAGARIVDHPAIAKISFTGSTAVGQSIARSAA 238

Query: 258 DSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317
           DS +K+V LE GGK ANIVF D  D+  A + TA GIF+NQGQ CIA +RL++ E++ DE
Sbjct: 239 DS-LKQVHLELGGKGANIVFDDA-DMAAAVNGTAFGIFHNQGQACIAASRLIVHEAVKDE 296

Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAA 377
           FL  L    ++ + G P DPAT MG L    H D V S +   E +G  +L G +A    
Sbjct: 297 FLERLITLTRSIRLGDPKDPATEMGPLTSSQHRDRVMSHLALTEEEGGTVLTGGHAPQDR 356

Query: 378 AIG------PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
           A+       PTI V+  P++  ++EE+FGP +VV  F +E++AL++AND  YGLG  +WT
Sbjct: 357 ALADGFYVEPTI-VETVPDSRAAQEEVFGPFMVVHAFKTEDEALRIANDVAYGLGGGLWT 415

Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
           RDLSRAHR++R L+AG V+VN+Y   +   PFGG   SG GR+    A+ ++T  K  WI
Sbjct: 416 RDLSRAHRVARDLRAGMVWVNSYKRVNPGSPFGGVGVSGYGREMGFEAMREYTSPKATWI 475

Query: 492 SLEA 495
           +++A
Sbjct: 476 NIDA 479


Lambda     K      H
   0.317    0.133    0.389 

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: 608
Number of extensions: 29
Number of successful extensions: 5
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: 495
Length of database: 492
Length adjustment: 34
Effective length of query: 461
Effective length of database: 458
Effective search space:   211138
Effective search space used:   211138
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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:

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:

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:

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