GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Stenotrophomonas chelatiphaga DSM 21508

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase

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



>NCBI__GCF_001431535.1:WP_057507768.1
          Length = 454

 Score =  237 bits (604), Expect = 7e-67
 Identities = 141/429 (32%), Positives = 217/429 (50%), Gaps = 9/429 (2%)

Query: 48  AEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSG 107
           A I+  +QAA  A    W   +  ER AVLR +G  + ERK+++    + + GK   +  
Sbjct: 23  AGIEQRLQAAAGAFPA-WSATSLQERAAVLRAIGAQLRERKDDIQGAMTREMGKLK-VEA 80

Query: 108 SIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWK 167
             ++ + A    +++D+            +   +Y    P+G +  + PWN P+  +   
Sbjct: 81  LAEVEKCAAACEYYADHAADYLKPQLIDTEAQRSYVRYEPIGCVFAVMPWNFPIWQVFRF 140

Query: 168 LAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPD 227
           LAPA  AGN  ++K A   P  A ++ E+ R  G+PDGV +++H    N   A +     
Sbjct: 141 LAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGVFDVLHI--DNDQAADVLRDRR 198

Query: 228 VNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQ 287
           V A++ TG    G+ I A+A   LK+   ELGG +  V+  D++LD+ I+  +KS F N 
Sbjct: 199 VKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVVLDDADLDKAIDAAVKSRFDNS 258

Query: 288 GEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIK 347
           G+ C+   R  V     +AF E+FVA   E   GDP DA+T +  +   +  + +   ++
Sbjct: 259 GQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADARTTLAPMARADLRDELHKQVQ 318

Query: 348 LAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEV 407
            +V +G  +L GG+  +G   GY    T++  +        EE+FGPV  VI    E E 
Sbjct: 319 ASVAKGARVLAGGEPVDGSHAGY--PATVLDQVGPGMPAYDEELFGPVAAVIRVKDEAEA 376

Query: 408 LEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGR- 466
           L+  NDT +GL  SVWT D  R    A Q+E G  +VN+    D+R PFGG K+SG GR 
Sbjct: 377 LKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNSIVKSDVRLPFGGSKESGFGRE 436

Query: 467 --EGGLHSF 473
             E G+H F
Sbjct: 437 LAEHGIHEF 445


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: 480
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 486
Length of database: 454
Length adjustment: 33
Effective length of query: 453
Effective length of database: 421
Effective search space:   190713
Effective search space used:   190713
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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