Alignments for a candidate for hcrA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Pseudomonas fluorescens FW300-N2C3

Align 4-hydroxybenzoyl-CoA reductase HbaC subunit (EC 1.3.7.9) (characterized)
to candidate AO356_26665 AO356_26665 carbon monoxide dehydrogenase

Query= metacyc::MONOMER-17404
         (777 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26665
          Length = 999

 Score =  251 bits (641), Expect = 1e-70
 Identities = 226/759 (29%), Positives = 326/759 (42%), Gaps = 43/759 (5%)

Query: 38  GALVARILRSPISHGDIVRLDVSKALALDGVAAIVTGEDCAITYGVLPIA----MNEYPM 93
           G L A I+RSP +H  I  +D S AL + GV  ++ GED        P+     M  + +
Sbjct: 43  GTLHAAIIRSPHAHARITSVDFSSALLMKGVHGVLVGEDVKRWALPFPVGVRQPMEHWCV 102

Query: 94  ARDRVRYRGEPVAAVAAVDAETARQALDLIELELRELPAYYESEAARAPDAWLLHDNKPG 153
           A D+VRY GEPVA V A     A  A++ + +E   LP   + E A A  A +LH+    
Sbjct: 103 AVDKVRYVGEPVAVVIAESRYLAEDAIEGVRVEYEPLPPIIDPERATAEQAPILHEAVGS 162

Query: 154 NIEREVHNEFGDLAAGFEAADLIRTHTHHCAEVNHAQIEPHACLMDYDPVTGRLTAQSVS 213
           N+  E    +G+    FE A    +        +   IE +  L  Y+  TG     +  
Sbjct: 163 NVVNERRFRYGEPEQAFEQAPHKVSLKVKFPRSSCTPIECYVVLAQYERATGIYDVLANF 222

Query: 214 QVGYYLHLMLARCLEIDPSRVRVIKP-FVGGGFGARVEVLNFEVIAALLARKASGRVLMR 272
           Q  Y LH ++AR L +  +R+R+  P   GG FG +  V  + V+  L +RK    V   
Sbjct: 223 QGPYALHTVMARALNVPGNRLRLRTPKDSGGSFGIKQGVFPYVVMMGLASRKVGAPVKWV 282

Query: 273 LSREETFITHRARPQTDITLTIGTRRDGRFTACSCEVVQRGGAYAGYGIVTILY-AGALL 331
             R E      +       +      DGR TA   + +   GAY         Y     L
Sbjct: 283 EDRLEHLQGASSATNRVTEIEAAVEADGRITALRYDQIDDCGAYLRAPEPATFYRMHGNL 342

Query: 332 QGLYDIPAVKYDGYRVYTNLPPCGAMRGHGSVDVRHAFENLVDRMARELGLDPFAVRRAN 391
            G Y I  ++     V TN  P G  RG G   V  A E L+  +A +L LDP  V R N
Sbjct: 343 TGAYAIRNLQVRNRVVLTNKTPSGLNRGFGGPQVYFALERLMQHIAVQLKLDPLDVIRRN 402

Query: 392 LLAA---PTRTLNDLMVNSYGLAECLDKVERASGWHERIGRLPPGK------GLGMAC-- 440
           L+ A   P R     +++S      +       G  E + R    +      G+G A   
Sbjct: 403 LVPADAFPYRAAAGALLDSGNYQAGIALAAADGGLDELLKRRDQARAEGRIYGIGYAAVI 462

Query: 441 ------SHYVSGSAKP--IHFTGEPHAVVA---LRLDFDGGITALTGAADIGQGSSTVVA 489
                   Y++ +  P      G  +  VA   + +   G ++    +A  GQG  T VA
Sbjct: 463 EPSISNMGYITTAMTPEERRKAGPKNGAVATATINVGPLGDVSVHVSSAPQGQGHQTTVA 522

Query: 490 ITVAETLGVALNRVRVISGDSAITPKD-----NGAYSSRITFMVGNAAIDAATKLKQILI 544
             VAE LGVAL    ++      T KD     +G YSSR    V  A   AA K++  L 
Sbjct: 523 QVVAEVLGVALE--SIVVNVELDTQKDAWSIASGNYSSRFAGAVAGAVYKAALKIRDRLA 580

Query: 545 AAAARKLEAVPEQIECAGESFFIGSGAQAA----LGFAEVVKAALVDEGAI--TVKGIFT 598
           A AA +L+A PE I  AG   F+ +G   A    +  A      L+ EG      +  F 
Sbjct: 581 AIAAEQLQASPEDIRFAGGKIFVVNGGAVAPFHRIAGATHWSPGLLPEGESGGLRETAFW 640

Query: 599 CPPESQGGQHRGGAVGSTMGFSYAAQVVEVSVDDATGLITVDKVWAALDCGRAINPLAVV 658
            PP+      +   V S++ + +   +  + +D  TG I +D+     D GR +NP  V 
Sbjct: 641 SPPQLVAPDDQ-DQVNSSLCYGFVFDICGLEIDRMTGEIHIDRYVTCHDAGRLLNPALVD 699

Query: 659 GQVQGAVWMGMGQAMCEETRY-LDGLPAHASFLEYRMPTMIESPPIEVAIVESVDPFGPF 717
           GQ++G    G+G A+ EE  Y  DG     +F +Y +PT  E+    +  +E+  PF P 
Sbjct: 700 GQIRGGFTQGLGAALMEEFAYGEDGSFLSGTFADYLVPTAPEAIEPVILHMETPSPFTPL 759

Query: 718 GAKEASEGALAGFPPAMVNAVANAIGIDLDDLPATPDRV 756
           GAK   EG     P  + NAVA+A+G     LP TP +V
Sbjct: 760 GAKGVGEGNNMSTPVCIANAVADALGRSDIRLPLTPSKV 798


Lambda     K      H
   0.320    0.136    0.402 

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: 1863
Number of extensions: 102
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 777
Length of database: 999
Length adjustment: 43
Effective length of query: 734
Effective length of database: 956
Effective search space:   701704
Effective search space used:   701704
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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