Alignments for a candidate for paaH in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Xenophilus azovorans DSM 13620

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_038214718.1 Q392_RS25280 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_000745855.1:WP_038214718.1
          Length = 709

 Score = 1059 bits (2738), Expect = 0.0
 Identities = 522/699 (74%), Positives = 606/699 (86%)

Query: 6   SADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFI 65
           SA V+     G+VL +TID+ PVNA+S+ VRRGL  A+EAADAD  V+A+LIVG G NF+
Sbjct: 8   SAAVIRSARHGEVLCITIDNPPVNAISSAVRRGLKEAVEAADADAGVKAILIVGEGANFV 67

Query: 66  AGADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAK 125
           AGADIREFG+ P PPSLP+VCNRIE C KPVVAAI GAALGGGLE+ALAAH+R+A+  A+
Sbjct: 68  AGADIREFGQAPQPPSLPEVCNRIEDCAKPVVAAIRGAALGGGLEIALAAHWRVALADAR 127

Query: 126 LGLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDIL 185
           LGLPEVQLGL+PGAGGT R PRL GAQAALDL+LSGRH  AKEAL+ GL+DR+   +D  
Sbjct: 128 LGLPEVQLGLMPGAGGTVRAPRLAGAQAALDLMLSGRHVKAKEALSLGLVDRIADGEDAQ 187

Query: 186 AEGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAV 245
           A GLAY +ELLA  A VRRTRDA  L+DRAA+ AA+  A+A+TAKKSRGLFSP+KIV+AV
Sbjct: 188 AAGLAYANELLAQGAGVRRTRDAQGLADRAAAQAAIDAAKADTAKKSRGLFSPMKIVEAV 247

Query: 246 EAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKPRTLNTIGV 305
           + A+++PF+E +++ER+ FL CIDSPQRAGLIHAFFAEREV K PE +AA+PR LN++G+
Sbjct: 248 QTALDKPFEEAVKLEREAFLACIDSPQRAGLIHAFFAEREVAKVPEAKAAQPRVLNSVGI 307

Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365
           VGGGTMGAGIAV+ LDAGLPV M+ERD  S+ RGRA++EKVYDGLI KGR++ E KAA+M
Sbjct: 308 VGGGTMGAGIAVSALDAGLPVVMVERDQPSIERGRANVEKVYDGLIRKGRMTPEAKAAVM 367

Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425
           +R++G+T Y ALA  DLVIEAVFED+ VK+AVF ELDRVCKAGAVLATNTSYLDIDA+A+
Sbjct: 368 ARYTGATDYAALADVDLVIEAVFEDIEVKKAVFKELDRVCKAGAVLATNTSYLDIDAIAA 427

Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485
           S SRP DVIGLHFFSPANIMKLLE+VVP +VSADVV+TAF LAKK++K PVRAGVCDGFI
Sbjct: 428 STSRPQDVIGLHFFSPANIMKLLEIVVPAKVSADVVSTAFALAKKMKKVPVRAGVCDGFI 487

Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAAT 545
           GNR+LAVY+ AAD +MEDGASPY+ID AVR FG+PMGPFQV DLAGGDIGWA RKRRAAT
Sbjct: 488 GNRILAVYKQAADYIMEDGASPYEIDEAVRGFGYPMGPFQVTDLAGGDIGWATRKRRAAT 547

Query: 546 RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPR 605
           R+P ARYV++ADR+CERGWFGQK+GRGFYLYPEG+R G PDPEV AI+DAER + GITPR
Sbjct: 548 RDPKARYVEVADRVCERGWFGQKTGRGFYLYPEGARVGQPDPEVLAIVDAERQKKGITPR 607

Query: 606 SFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGL 665
            FT EEI+RRYMAAM+NEGA VV E IALRPLDVDVTFLYGYGFPR+RGGPMKYADMVGL
Sbjct: 608 QFTAEEIMRRYMAAMVNEGAKVVEEGIALRPLDVDVTFLYGYGFPRHRGGPMKYADMVGL 667

Query: 666 PKILADIREFAKEDPLFWKPSPLLIELVERGADFASLNQ 704
           PKIL DIR FAKEDPLFWKP+PLL +LV  G DFASLNQ
Sbjct: 668 PKILEDIRAFAKEDPLFWKPAPLLEKLVAEGRDFASLNQ 706


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: 1418
Number of extensions: 57
Number of successful extensions: 1
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: 709
Length adjustment: 39
Effective length of query: 667
Effective length of database: 670
Effective search space:   446890
Effective search space used:   446890
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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