Alignments for a candidate for paaH in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Desulfacinum infernum DSM 9756

Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_073041507.1 BUB04_RS16430 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::P28793
         (715 letters)



>NCBI__GCF_900129305.1:WP_073041507.1
          Length = 681

 Score =  307 bits (786), Expect = 1e-87
 Identities = 206/661 (31%), Positives = 335/661 (50%), Gaps = 36/661 (5%)

Query: 30  NKFNRLTLNELRQAVDAIKADASVKGVIVSSGKDVFIVGADITE--FVENFKLPDAELIA 87
           N F+   L  L +A++ + A+  VKG++++    +F  GAD+T+  FV  F+       A
Sbjct: 35  NVFSEAALQSLNEAINKVLAEGDVKGLMLTGKPYIFAAGADLTQVPFVTTFEQGYQIGKA 94

Query: 88  GNLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADFRVMADSAK-IGLPEVKLGIY 146
           G+    ++     DL  PTVAA NG+ALGGGLE+ L  D+R +A S   +G PE  +G+ 
Sbjct: 95  GHTIMKRLM----DLPFPTVAAYNGVALGGGLEIGLYCDYRTVAKSVPAMGFPECFIGLI 150

Query: 147 PGFGGTVRLPRLIGVDNAVEWIASGKENR-----AEDALKVSAVDAVVTADKLGAAALDL 201
           PG+GG     +L+G + A+E I     N+        A ++   D +    +    +L  
Sbjct: 151 PGWGGCTLATKLLGPEKALELIVFNALNQNRMINGPQAFEIGIADRLFDGAEFFDESLQF 210

Query: 202 IKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGFVAGQAGPNYPAPVEAIKTIQK 261
           +   ISG+ +   +  PK   LK        A   AK FV  +     PAP  AI+ I+ 
Sbjct: 211 LVNIISGK-EKVERPAPKTANLKA-------AVSKAKAFVDSKVHGAAPAPYRAIELIEG 262

Query: 262 AANFGRDKALEVEAAGFAKLAKTSASNCLIGLF-LNDQELKKKAKVYDKIAKDVKQAAVL 320
           A  +  D+  E E      L K+    C I  F L ++  KK   + D   K VK+  ++
Sbjct: 263 AVKWDIDQGFEEENKALGDLVKSRQCKCSIYAFDLVNRYAKKVKGIPDVKPKPVKKVGII 322

Query: 321 GAGIMGGGIAYQSASK-GTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTPAKMAEVL 379
           GAG+M   +A     + G P++MKDI +  +++G+A         V+KGRM  A+   + 
Sbjct: 323 GAGLMASQLAQVFIYRLGVPVVMKDIKQEFVDKGVAYVRGEFQKMVEKGRMPEARARYLS 382

Query: 380 NGIRPTLSYGDFGNVDLVVEAVVENPKVKQAVLAEVENHVREDAILASNTSTISISLLAK 439
           + +  TLSY DF + D V+EAV E   +K+ V AEVE  V  + ILA+NTS++S++ +  
Sbjct: 383 SLVHGTLSYDDFADCDFVIEAVFERMDIKKQVFAEVEAVVSPECILATNTSSLSVTEMGS 442

Query: 440 ALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGFL 499
            LK P+  +G HFFNPV ++PLVEVI+  ++ D  +AT    AKK+ K  ++V D P FL
Sbjct: 443 DLKHPQRVIGFHFFNPVAVLPLVEVIKTPQTDDQTLATAFDLAKKLKKTGVLVKDAPAFL 502

Query: 500 VNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEG 559
           VNR+L         +V  G DF+++D+ +   G PM P  L+ +VG    +H  + +   
Sbjct: 503 VNRLLTKMLSDCLTMVDEGADFIQVDEALLALGMPMAPFDLLALVGFPVAYHVCETLNRA 562

Query: 560 FPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQKKLVDSSVLEVLKPIVYEQ 619
           F        R  ++A +  K+L        Y       G + K V+  V ++ +      
Sbjct: 563 F-----GPERFPLNANF--KKLIDAGINSIYV-----PGSKVKKVNPEVEKLWEK--KGD 608

Query: 620 RDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVYGIGFPLFRGGALRYIDSIG 679
           ++   ++I + ++  L  E    L++ +V+++ + D+ ++ G G+P F GG   Y+D  G
Sbjct: 609 KEFHPDEIRDRVLSNLAKEIDLILKEKVVDSSRDVDLAMIMGAGWPFFMGGITMYLDMAG 668

Query: 680 V 680
           +
Sbjct: 669 I 669


Lambda     K      H
   0.318    0.137    0.386 

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: 1140
Number of extensions: 59
Number of successful extensions: 8
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: 715
Length of database: 681
Length adjustment: 39
Effective length of query: 676
Effective length of database: 642
Effective search space:   433992
Effective search space used:   433992
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: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources