Alignments for a candidate for paaH in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Stutzerimonas stutzeri A1501

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_011911348.1 PST_RS00510 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>NCBI__GCF_000013785.1:WP_011911348.1
          Length = 701

 Score =  638 bits (1645), Expect = 0.0
 Identities = 332/693 (47%), Positives = 458/693 (66%), Gaps = 2/693 (0%)

Query: 8   DVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAG 67
           DV+  E RG + L+ +++ PVNAL   VR+GLL A   AD    V AV++V  G  F+AG
Sbjct: 3   DVIRLERRGDIALILVNNPPVNALGHAVRKGLLDAFRQADEAPEVTAVVLVCEGPTFMAG 62

Query: 68  ADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLG 127
           ADI+EFGKPP  PSLP+V   IE C KP VA IHG+ALGGGLEVAL  HYRIA   AK+G
Sbjct: 63  ADIKEFGKPPQAPSLPEVIEVIEGCRKPSVAVIHGSALGGGLEVALGCHYRIARSDAKVG 122

Query: 128 LPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE 187
           LPEV+LGLLPGAGGTQR PRL G + AL++I+SG+   A EAL   ++D L   D ++  
Sbjct: 123 LPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPIGAAEALEHHIVDELFEGD-LIEA 181

Query: 188 GLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEA 247
           GL Y   L+      RR+ +     +   + A +    AE AK+  GLFSPL+ + AVEA
Sbjct: 182 GLTYARRLVEEGRGPRRSGEQTRGLEGVDNEALIRAKHAEVAKRMPGLFSPLRCIAAVEA 241

Query: 248 AIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVV 306
           A   P  EGL+ ER+LF EC++SPQR  LIH+FFAER+  K  +  +  K R + T  V+
Sbjct: 242 ATRLPLAEGLKRERELFTECLNSPQRGALIHSFFAERQAGKIDDLPSDVKLRPIRTAAVI 301

Query: 307 GGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMS 366
           GGGTMG GIA++  + G+PV ++E +D +L RG     + Y   + +G L+ +     ++
Sbjct: 302 GGGTMGVGIALSFANTGVPVKLLEINDEALQRGLQRARETYAASVKRGSLTEDAMEQRLA 361

Query: 367 RWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASS 426
             +G T Y ALA AD+V+EAVFE++ VKQ VF +LD VCK GA+LA+NTS LD++A+A+ 
Sbjct: 362 LIAGVTDYGALADADVVVEAVFEEMGVKQQVFEQLDAVCKPGAILASNTSSLDLNAIAAF 421

Query: 427 VSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIG 486
             RP DV+GLHFFSPAN+M+LLEVV  ++ S +V+ATA  + K+L+K  V  GVCDGF+G
Sbjct: 422 TKRPEDVVGLHFFSPANVMRLLEVVRGERTSDEVLATAMAIGKQLKKVSVVVGVCDGFVG 481

Query: 487 NRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATR 546
           NR++  Y   A+ ++E+GA+P Q+DAA+R FG  MGPF + DL+G DIG A RKR+ AT 
Sbjct: 482 NRMVFQYGREAEFLLEEGATPQQVDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQRATL 541

Query: 547 NPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRS 606
                +  ++D+LC  G  GQK+G G+Y Y  G+R+   +P++  +++A     GI  ++
Sbjct: 542 PAHLDFPTVSDKLCAAGMLGQKTGAGYYRYEPGNRTPQENPDLAPMLEAASREKGIERKA 601

Query: 607 FTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLP 666
             ++ I+ R + A++NEGA ++ E IA R  D+DV +L GYGFP +RGGPM YAD VGL 
Sbjct: 602 LDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAFRGGPMYYADSVGLD 661

Query: 667 KILADIREFAKEDPLFWKPSPLLIELVERGADF 699
           K+LA ++E       +WKP+PLL +L   G  F
Sbjct: 662 KVLARVKELHARCGDWWKPAPLLEKLAAEGRTF 694


Lambda     K      H
   0.320    0.136    0.392 

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: 1156
Number of extensions: 42
Number of successful extensions: 3
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: 706
Length of database: 701
Length adjustment: 39
Effective length of query: 667
Effective length of database: 662
Effective search space:   441554
Effective search space used:   441554
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: 54 (25.4 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:

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 2024 update 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