GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pontimonas salivibrio CL-TW6

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_104913707.1 C3B54_RS06115 gamma-aminobutyraldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_002950575.1:WP_104913707.1
          Length = 478

 Score =  294 bits (752), Expect = 5e-84
 Identities = 175/475 (36%), Positives = 261/475 (54%), Gaps = 15/475 (3%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +FI+G++V S   +T   ++PATEE         AA++D A QAA KA  G W + T  E
Sbjct: 8   NFINGQYVDSKGSETIPLVDPATEEVYAHSPISSAADVDDAYQAASKAFEG-WSETTPAE 66

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R   L ++ D + +R EE + LES D GKP       +I  +     FF+   R +  ++
Sbjct: 67  RQLALFRIADELEKRGEEFADLESQDAGKPRASLVEDEISLSVDQIRFFAGAARNLEGKS 126

Query: 133 T--QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTA 190
               M D   ++  R P+GV+G + PWN PL +  WK APA+AAGNT V+KP++ TP + 
Sbjct: 127 AGEYMKDHT-SFIRREPIGVVGQVAPWNYPLNMAVWKFAPAVAAGNTTVLKPSDTTPQST 185

Query: 191 TVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT 250
            +LAEIC    +P+GVVN++ G    + G A+ +H     +S TG    G  +  +AA  
Sbjct: 186 LLLAEICA-MHLPEGVVNVITG--DRTTGGAMIDHKIPEMVSITGSVRAGLEVAKAAATD 242

Query: 251 LKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF--- 307
           LKR+  ELGGK P ++F D+++   IE    + + N G+ C   +R+ V    ++ F   
Sbjct: 243 LKRVHLELGGKAPVIVFDDADIPSAIEGIGIAGYFNAGQDCTAATRVVVHESIHDEFIAE 302

Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLE 367
           L+K+VA    +  G P D  T  G + +    +RV G +   +    T+  GG R    E
Sbjct: 303 LKKWVAAN--VTTGLPSDPNTFYGPVNNANQMDRVMGILG-ELPSHSTVEAGGVRQG--E 357

Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427
           +GYF+EPTI++GL ++   ++ EIFGPV+TV PF TEEE +   N   YGLS+SVWT D 
Sbjct: 358 RGYFIEPTIVSGLKQNDAAIQTEIFGPVITVQPFRTEEEAMTMANGVPYGLSSSVWTKDH 417

Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482
            RA R A  ++ G VW+N         P GG K SG G++   + FE Y+ + ++
Sbjct: 418 ARAMRFAKGLDFGAVWINCHIPLVAEMPHGGFKHSGHGKDLSQYGFEEYTRVKHV 472


Lambda     K      H
   0.318    0.136    0.404 

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: 575
Number of extensions: 28
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: 486
Length of database: 478
Length adjustment: 34
Effective length of query: 452
Effective length of database: 444
Effective search space:   200688
Effective search space used:   200688
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