Alignments for a candidate for fadB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Marinobacter adhaerens HP15

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate GFF4001 HP15_3941 fatty oxidation complex alpha subunit

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



>FitnessBrowser__Marino:GFF4001
          Length = 702

 Score =  658 bits (1698), Expect = 0.0
 Identities = 347/701 (49%), Positives = 471/701 (67%), Gaps = 10/701 (1%)

Query: 7   ADVVSRELRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIA 66
           ++VVS    G + ++T+++ PVNAL   VR GLLAA+E    D    A+L+V  GR FIA
Sbjct: 7   SEVVSYNREGNIGVITVNYPPVNALGQAVRSGLLAALEQGQKDTEARALLLVCEGRTFIA 66

Query: 67  GADIREFGKPPVPPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKL 126
           GADIREFGKP   P+LP + N  E   KP+VAAIHG ALGGGLE AL+ HYR+A+  AK+
Sbjct: 67  GADIREFGKPMQEPTLPTLVNTFENSDKPLVAAIHGTALGGGLETALSCHYRVAISSAKV 126

Query: 127 GLPEVQLGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILA 186
           GLPEV+LGLLPGAGGTQR PRL GA+ AL++I +G    AK+ALA G++D +   DDI A
Sbjct: 127 GLPEVKLGLLPGAGGTQRLPRLTGARKALEMITTGEFVGAKDALALGILDAVEEGDDIRA 186

Query: 187 EGLAYVHELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVE 246
            G+AY  +++    PVRR RD     +           R E  K++RGLFSP K VDAVE
Sbjct: 187 VGMAYAQKVVDEGKPVRRVRDITDKIEADKGSDVFDQFRDELKKRARGLFSPFKCVDAVE 246

Query: 247 AAIEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLKAPETRAAKP-RTLNTIGV 305
           AA   PFDEG++ ER+LF+EC++SPQRAGLIH+FF EREV K        P R + ++G+
Sbjct: 247 AAFNLPFDEGMKRERELFMECMESPQRAGLIHSFFGEREVSKVKGLSKDTPVRDVKSVGI 306

Query: 306 VGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALM 365
           +G GTMG GIA+  ++ G+PVT++E    +L +G A I + Y+    KG+L+ E+    M
Sbjct: 307 IGAGTMGGGIAMNFVNVGIPVTIVEVKQEALDKGLAIIRRNYENSAKKGKLTQEQVEQRM 366

Query: 366 SRWSGSTSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALAS 425
           +  + S +YD     DLVIEAVFE++A+K+ +FA+LD VCK GA+LA+NTS LDID +AS
Sbjct: 367 ALITPSLTYDDFRDVDLVIEAVFENMAIKKEIFAKLDEVCKPGAILASNTSTLDIDEIAS 426

Query: 426 SVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFI 485
           +  RP DV+G+HFFSPAN+MKLLE V   + S +V AT   +AKK++K  V  G C GF+
Sbjct: 427 ATKRPEDVVGMHFFSPANVMKLLENVRGSKTSDEVKATVMAVAKKIKKVGVMVGNCYGFV 486

Query: 486 GNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAAR-KRRAA 544
           GNR+L    + A +++++GA+P Q+D  +   GFPMG F + DLAG D+G+  R +RR A
Sbjct: 487 GNRMLHKRGTEAMSLVDEGATPQQVDKVLTDLGFPMGQFAMSDLAGIDVGYRIREERRKA 546

Query: 545 TRNPAARYVQIADRLCERGWFGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITP 604
             +  A ++   D+L E+G  GQK+  G Y Y EGSR   PDPEVE +I+  R   GITP
Sbjct: 547 GEDIPASWM---DKLAEQGRLGQKTQAGVYKYEEGSRKPIPDPEVEQLIEQFRKEQGITP 603

Query: 605 RSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVG 664
           R  T++EI+ R +  MINEGA ++ E IA RPLD+D+ ++YGYGFP YRGGPM +AD  G
Sbjct: 604 REITNQEILERCVYVMINEGAKILEEGIADRPLDIDIVWIYGYGFPAYRGGPMFWADQEG 663

Query: 665 LPKILADIREFAKEDPL---FWKPSPLLIELVERGADFASL 702
           L  IL+ ++++  +D +    W+P+ LL +LV  G  FA L
Sbjct: 664 LDTILSAVKKY--QDTVGGEQWEPAALLEKLVAEGRKFADL 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: 1115
Number of extensions: 43
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: 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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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 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