Alignments for a candidate for fadB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_068172592.1 HTA01S_RS13945 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

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



>NCBI__GCF_001592305.1:WP_068172592.1
          Length = 702

 Score =  597 bits (1538), Expect = e-175
 Identities = 322/704 (45%), Positives = 452/704 (64%), Gaps = 24/704 (3%)

Query: 13  ELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIRE 72
           ++ G V ++T+++ PVN L    R+ + A +E A+AD AV+A+++ GAG+ F  GADIRE
Sbjct: 6   QVHGDVAVITLNNPPVNGLGLSTRQAITAGLEKAEADPAVKAIVLTGAGKAFSGGADIRE 65

Query: 73  FGKPPV--PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPE 130
           FG P     P+L  V   +E  +KPVVAA+H   +GGGLE+AL AHYRIA  G  + LPE
Sbjct: 66  FGSPKAIQEPNLLSVILAVENTSKPVVAAVHSVCMGGGLELALGAHYRIAAPGCNVALPE 125

Query: 131 VQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFG---LIDRLGSSDDILAE 187
           V+LGL+PGAGGTQR PR++G +AAL++I+SG    ++         L D+L +S + LAE
Sbjct: 126 VKLGLIPGAGGTQRLPRVLGVEAALNMIVSGEPVKSEMLAQLPGQKLFDKLAASPESLAE 185

Query: 188 -GLAYVHELLAAHAPVRRTRDAAALS-------DRAASLAAVATARAETAKKSRGLFSPL 239
             LA+  E+ A HA      D  AL              A    AR      ++   +P 
Sbjct: 186 EALAFAREVAAKHA------DGFALPLVRNLPCKHKDGDAYFQFARNMVKGMAKNFPAPP 239

Query: 240 KIVDAVEAAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-R 298
           K VDAVEAA ++ F +G+  ER+ F+  + +P+   L H F AER   K P+     P R
Sbjct: 240 KCVDAVEAATKKKFADGMAFERETFINLMWTPECRSLRHLFVAERAASKIPDVPEDTPQR 299

Query: 299 TLNTIGVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSA 358
           ++ ++ V+G GTMG GI +  L+AG+PV ++E    +L RG A I K Y+  + KG+L A
Sbjct: 300 SIQSVAVIGAGTMGGGITMNFLNAGIPVKVLEMKQDALDRGVATIRKNYEAQVKKGKLKA 359

Query: 359 EKKAALMSRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYL 418
           +K    MS  S + SYD +  ADLVIEAVFE++ VK+AVF ELDRV K GA+LA+NTS L
Sbjct: 360 DKYEQRMSLLSTTLSYDDIGLADLVIEAVFEEIGVKEAVFKELDRVMKPGAILASNTSTL 419

Query: 419 DIDALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRA 478
           D++ +AS   RP DV+GLHFFSPAN+MKLLEVV  ++ + DV+AT   +AKK++KT V +
Sbjct: 420 DVNKIASFTQRPQDVVGLHFFSPANVMKLLEVVRGEKTAKDVMATVMTVAKKIKKTAVVS 479

Query: 479 GVCDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAA 538
           GVCDGFIGNR++  Y      ++++G +P Q+D A+  FG  MGPF++ DLAG DIGWA 
Sbjct: 480 GVCDGFIGNRMIEQYGRQGGFLLDEGCTPEQVDKAMEKFGMAMGPFRMGDLAGNDIGWAI 539

Query: 539 RKRRAATRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERA 598
           RKRR   + P  +Y + AD LCE+G FGQK+G G+Y Y  G R   P+ EV  +I+  R 
Sbjct: 540 RKRRYQEK-PDMKYSKTADLLCEKGRFGQKTGAGWYDYVPGKRDAIPNAEVVQMIEDHRK 598

Query: 599 RAGITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMK 658
             GITPR  +DEEI++R + +++NE A+++ E IA +  D+DV +++GYGFP YRGGP+ 
Sbjct: 599 ALGITPRKISDEEIVQRLVFSLVNEAAHILEEGIANKASDIDVVYIFGYGFPVYRGGPLN 658

Query: 659 YADMVGLPKILADIREFAK---EDPLFWKPSPLLIELVERGADF 699
           YA+ VGL  ++  ++ FAK   +D  FW+P+PLL  L E G  F
Sbjct: 659 YANEVGLFNVVQAMKRFAKNPLDDAKFWQPAPLLARLAEEGKTF 702


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: 1046
Number of extensions: 34
Number of successful extensions: 7
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: 702
Length adjustment: 39
Effective length of query: 667
Effective length of database: 663
Effective search space:   442221
Effective search space used:   442221
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