GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Escherichia coli BW25113

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 15565 b1444 medium chain aldehyde dehydrogenase (NCBI)

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



>lcl|FitnessBrowser__Keio:15565 b1444 medium chain aldehyde
           dehydrogenase (NCBI)
          Length = 474

 Score =  330 bits (845), Expect = 8e-95
 Identities = 187/473 (39%), Positives = 277/473 (58%), Gaps = 8/473 (1%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74
           I+G+ V S +G+     NPAT + L  +AE  A ++D AV+AA  A    W + T   R 
Sbjct: 7   INGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAF-AEWGQTTPKVRA 64

Query: 75  AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQ 134
             L K+ D+I E  +  + LES + GKP   + + +IP     F FF+   R +   A  
Sbjct: 65  ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124

Query: 135 MDDVALNYAIRR-PVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193
                    IRR P+GV+  I PWN PL++  WKLAPALAAGN VV+KP+E+TP+TA  L
Sbjct: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184

Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKR 253
           AE+ +D   P GV+N++ G G  + G  LT HP V  +S TG   TG+ I++  A ++KR
Sbjct: 185 AELAKDI-FPAGVINILFGRG-KTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKR 242

Query: 254 LSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVA 313
              ELGGK P ++F D++++ V+E      + N G+ C    RIY ++  Y+  +EK  A
Sbjct: 243 THMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGA 302

Query: 314 KTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGT-ILTGGKRPEGLEKGYFL 372
               L  G P D  T++G L S  H ERV   ++ A   G   ++TGG++ +G   GY+ 
Sbjct: 303 AVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG--NGYYY 360

Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432
            PT++ G  +D  +V++E+FGPVV+V PFD EE+V+   ND+ YGL++SVWT D+ RAHR
Sbjct: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420

Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIK 485
           V+ +++ G  WVNT F+     P GG K SG G++  L+  E Y+ + ++ +K
Sbjct: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473


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: 569
Number of extensions: 25
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: 474
Length adjustment: 34
Effective length of query: 452
Effective length of database: 440
Effective search space:   198880
Effective search space used:   198880
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 Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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