GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Limnohabitans curvus MWH-C5

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_108359063.1 B9Z44_RS11550 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_003063475.1:WP_108359063.1
          Length = 477

 Score =  313 bits (802), Expect = 8e-90
 Identities = 182/475 (38%), Positives = 274/475 (57%), Gaps = 11/475 (2%)

Query: 21  RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80
           ++FING+   A   +  + + PV      +I RG+  D+D A++AA    +   W   + 
Sbjct: 3   KMFINGQSVNALSGKVLDVLSPVDGQKFEEIPRGEKADVDLAVNAANKALDSA-WGKMTA 61

Query: 81  AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140
            +R  +L KL + +  H  ELA LE  DTGKP+  + + DI   AR   +Y    DK++G
Sbjct: 62  LERGRLLMKLGEKVLEHHAELAALEARDTGKPMT-TAKTDITVLARYFEFYGSGADKIHG 120

Query: 141 EVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200
            V          ++REP+GV A I+PWN+P  +    + PALA GN+V++KP+E + L+ 
Sbjct: 121 LVLPFLDGYTVNVLREPLGVTAHIIPWNYPAQMLGRSIAPALAMGNAVVVKPAEDACLTP 180

Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260
           IR+A LA++ G PDG +N+VTG G EAG ALS H  I+ I+FTGS   G  L++ A   N
Sbjct: 181 IRVAELARDVGFPDGAINIVTGLGEEAGAALSEHPGINFISFTGSNEVG-VLIQKAAAKN 239

Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320
           + +  LE GGKS ++VF D  DL +A      GI  N GQ C AG+RL++++SI  E + 
Sbjct: 240 VIKCVLELGGKSPHVVFGDA-DLDRAVPIITRGIIANTGQTCTAGSRLIVQKSIYPEIME 298

Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDG-RNAGLAAA 378
            L +Q    + G P D     G +++ A  D V  F++E E  G +++  G  + GL   
Sbjct: 299 RLAKQFAQIKVGTP-DMDLDCGPVVNIAQRDRVAYFLKEAEKSGIEMVAQGVLSPGLPKE 357

Query: 379 ---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLS 435
              + PT+  +V  N   ++EEIFGPVL    F +E + + LAN + +GL AAVWT +  
Sbjct: 358 GYYVTPTLLGNVPANHRCAQEEIFGPVLAAMSFDTEAEGIALANGTDFGLMAAVWTENGG 417

Query: 436 RAHRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489
           R  R+S+ +KAG V++N +   G + +PFGG K+SG+GR+K   ALE+ +  KT+
Sbjct: 418 RQQRVSKAIKAGQVYINAFGAGGGVELPFGGVKRSGHGREKGFLALEEVSTTKTV 472


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: 554
Number of extensions: 25
Number of successful extensions: 7
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: 477
Length adjustment: 34
Effective length of query: 461
Effective length of database: 443
Effective search space:   204223
Effective search space used:   204223
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.

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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:

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