Alignments for a candidate for paaH in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Tistlia consotensis USBA 355

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_085121628.1 B9O00_RS06390 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

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



>NCBI__GCF_900177295.1:WP_085121628.1
          Length = 707

 Score =  610 bits (1574), Expect = e-179
 Identities = 341/702 (48%), Positives = 447/702 (63%), Gaps = 15/702 (2%)

Query: 8   DVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAG 67
           D V     G V +VTI + PVNAL   VR G++AA+E A AD AV+AV++ GAGR F  G
Sbjct: 10  DAVGYSTDGDVAVVTIANPPVNALGYAVRSGIVAALERAAADPAVKAVVLTGAGRTFSGG 69

Query: 68  ADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLG 127
           ADI EFGKPP  P L  V    E+  KPVVAAI G ALGGGLE+ALA H R+A   A+LG
Sbjct: 70  ADITEFGKPPREPGLSAVIRHCESLAKPVVAAIRGVALGGGLELALACHARVAAPDARLG 129

Query: 128 LPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAE 187
           LPEV+LGLLPGAGGTQR PR++G +AA+++I++G   +A +A   GL+D +   DD++A 
Sbjct: 130 LPEVKLGLLPGAGGTQRLPRVVGPEAAVEMIVTGTPIAAAKAATLGLVDGI-VEDDLVAG 188

Query: 188 GLAYVHELLAAH---APVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDA 244
             A+   L+ +     PVR   D  A + R  S  A      +  +++RGL +PL  V A
Sbjct: 189 ATAHARALVESRQTPVPVRDREDRLAATRRDPS--AFEAKAKQLTQRTRGLEAPLACVRA 246

Query: 245 VEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLK-APETRAAKPRTLNTI 303
           V  A++ PFDE L  ER LF E +D  Q     H FFAERE  K A   R   PR +  +
Sbjct: 247 VRMALDTPFDEALSRERALFTELLDGFQSKAQRHLFFAEREATKVAGVGREVTPRPVARV 306

Query: 304 GVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAA 363
           GVVG GTMG GIA+   +AG+PVT++E +  +L RG   I K YD  +A+G L  +++  
Sbjct: 307 GVVGAGTMGGGIAMTFANAGIPVTLVEMNREALERGLGVIRKNYDLSVARGSLGEQERDR 366

Query: 364 LMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDAL 423
            ++  +GST Y+ LA ADLVIEAVFE++AVK+ VF  LDR+ + GA+LA+NTSYLDIDA+
Sbjct: 367 RLALITGSTRYEDLAVADLVIEAVFEEMAVKKEVFGRLDRIARPGAILASNTSYLDIDAI 426

Query: 424 ASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDG 483
           A +  RPADV+G HFFSPAN+MKLLE+V  ++ + DV+AT   LAK++ K PV  GVC G
Sbjct: 427 ADATGRPADVVGTHFFSPANVMKLLEIVRGRRTAPDVLATLLGLAKRIGKVPVVVGVCHG 486

Query: 484 FIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRA 543
           F+GNR+LA   +  +A++ +GA P ++D A   FGFPMGPF + DLAG D+GW  RK   
Sbjct: 487 FVGNRMLAARSAENEALLLEGALPQEVDRAFTDFGFPMGPFAMGDLAGLDVGWRNRK--- 543

Query: 544 ATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGIT 603
                  R   IAD LCE G FGQK+G GFY Y  GSR   PDP VEA+I  +    GI 
Sbjct: 544 ----SLGRTAVIADALCEAGRFGQKTGEGFYRYEAGSRRPEPDPWVEALIAGKARERGIE 599

Query: 604 PRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMV 663
            R    EEI+ R +  MINEGA ++ E IA RP D+DV ++ GYGFP  +GGPM +AD V
Sbjct: 600 RRPIAAEEIVERTLYPMINEGARILEEGIAARPSDIDVAWVDGYGFPVGKGGPMFWADHV 659

Query: 664 GLPKILADIREF-AKEDPLFWKPSPLLIELVERGADFASLNQ 704
           GL  I+  + ++  K     +  +PLL  L   G  FA+L +
Sbjct: 660 GLATIVERLDDWHGKTGRELFAAAPLLRRLAADGGSFAALGR 701


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: 1248
Number of extensions: 54
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: 706
Length of database: 707
Length adjustment: 39
Effective length of query: 667
Effective length of database: 668
Effective search space:   445556
Effective search space used:   445556
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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