GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Pseudarthrobacter sulfonivorans Ar51

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase

Query= metacyc::MONOMER-15732
         (497 letters)



>NCBI__GCF_001484605.1:WP_058929223.1
          Length = 508

 Score =  400 bits (1029), Expect = e-116
 Identities = 218/488 (44%), Positives = 289/488 (59%), Gaps = 12/488 (2%)

Query: 16  ERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWS 75
           +R   M I   W  ++SG T +  +P      G VPAA  EDVDRAVRAAR+AFD+  W 
Sbjct: 18  DRSYSMLIDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWP 77

Query: 76  RLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWAT 135
           +  P +R  LL R ADL+  +A +LA  +   NGK         +Q+      Y+AG A 
Sbjct: 78  QTLPSQRAALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMG-QHAHYVAGLAE 136

Query: 136 KIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVL 195
            I+G T+E++ P         F  RE IGVV  I  WN PL+L  WKL  ALA G T+V+
Sbjct: 137 TIQGRTIESNWP-----NTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVI 191

Query: 196 KPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGK 255
           KP++ TP S L++AEL  EAG+P GV NVVTG G   G+AL  H GVDK+ FTGST  G+
Sbjct: 192 KPSEATPTSTLRMAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGR 251

Query: 256 LIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHR 315
            I K A +   RVTLELGGKSP I+  DA++  A  GA   IF   GQ C  GSR+ V  
Sbjct: 252 AINKQAAERFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQD 311

Query: 316 KHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGG- 374
             +D+ V  +A     + LG+ LDP V MGP+ +  Q  +V  Y++LG+  GA V  GG 
Sbjct: 312 SIYDDFVDRMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGA 371

Query: 375 -----EGFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGL 429
                     G F +PTV  +V    RL QEEIFGPV   + F D DE + +AN + +GL
Sbjct: 372 RCMTTSELSKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGL 431

Query: 430 GASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTE 489
            A +W+ND++  HRMI R++SG+VWVN +   + ++PFGG+K SG+GRE+G  A++ YTE
Sbjct: 432 AAGVWTNDVSRAHRMIRRVRSGTVWVNTYRLTNYSVPFGGFKQSGIGRELGPDALDAYTE 491

Query: 490 LKSVLIKL 497
           +KS  I L
Sbjct: 492 VKSAWIDL 499


Lambda     K      H
   0.320    0.137    0.413 

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: 628
Number of extensions: 33
Number of successful extensions: 4
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: 497
Length of database: 508
Length adjustment: 34
Effective length of query: 463
Effective length of database: 474
Effective search space:   219462
Effective search space used:   219462
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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