Alignments for a candidate for ech in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Marinobacter adhaerens HP15

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate GFF4001 HP15_3941 fatty oxidation complex alpha subunit

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Marino:GFF4001
          Length = 702

 Score =  198 bits (503), Expect = 8e-55
 Identities = 137/398 (34%), Positives = 211/398 (53%), Gaps = 27/398 (6%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSL-KEGVE 61
           V +IG+G MG GIA      G  V + ++  E L + +  I+ +     + G L +E VE
Sbjct: 304 VGIIGAGTMGGGIAMNFVNVGIPVTIVEVKQEALDKGLAIIRRNYENSAKKGKLTQEQVE 363

Query: 62  QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121
           Q +A I P        +  D VIEAV E++ +K+ IF   +    P A+LA+NTS+L I 
Sbjct: 364 QRMALITPSLTYDD-FRDVDLVIEAVFENMAIKKEIFAKLDEVCKPGAILASNTSTLDID 422

Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181
           EIAS  K P+ VVGMHFF+P  +M L+E VRG  TSDEV  T   +AK + K  ++V + 
Sbjct: 423 EIASATKRPEDVVGMHFFSPANVMKLLENVRGSKTSDEVKATVMAVAKKIKKVGVMVGNC 482

Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241
            GF  NR+L +       LV++G A+ Q+VD   + +LGFPMG F ++D  G+D+GY + 
Sbjct: 483 YGFVGNRMLHKRGTEAMSLVDEG-ATPQQVD-KVLTDLGFPMGQFAMSDLAGIDVGYRIR 540

Query: 242 KAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY------PSPGKFVRPTLPSTSKKL 295
           +     G +  P S  +KL  QG+LG K+ +G Y+Y      P P   V   +    K+ 
Sbjct: 541 EERRKAG-EDIPASWMDKLAEQGRLGQKTQAGVYKYEEGSRKPIPDPEVEQLIEQFRKEQ 599

Query: 296 G------------RYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---GILSYA 339
           G               +   +NE + +L EGI  +  D +   + G G P    G + +A
Sbjct: 600 GITPREITNQEILERCVYVMINEGAKILEEGIADRPLDIDIVWIYGYGFPAYRGGPMFWA 659

Query: 340 DEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           D+ G+D +++ +++ + T G + + P  LL  +V EG+
Sbjct: 660 DQEGLDTILSAVKKYQDTVGGEQWEPAALLEKLVAEGR 697



 Score =  114 bits (285), Expect = 1e-29
 Identities = 70/185 (37%), Positives = 108/185 (58%), Gaps = 12/185 (6%)

Query: 410 IVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPV 469
           I +N P   NA+   +   +  AL+  ++  + R + +  +GR F AGAD+ EFG     
Sbjct: 21  ITVNYPP-VNALGQAVRSGLLAALEQGQKDTEARALLLVCEGRTFIAGADIREFGK---- 75

Query: 470 KAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEINL 529
              +       +    +   KP++A I+G ALGGG+E ALS  +RVA  +A++G PE+ L
Sbjct: 76  --PMQEPTLPTLVNTFENSDKPLVAAIHGTALGGGLETALSCHYRVAISSAKVGLPEVKL 133

Query: 530 GLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRKLAN 588
           GL+PG GGTQRL RL+G RK LE++ TG  V A++A  LGI++ + E +    ++R +  
Sbjct: 134 GLLPGAGGTQRLPRLTGARKALEMITTGEFVGAKDALALGILDAVEEGD----DIRAVGM 189

Query: 589 AIAEK 593
           A A+K
Sbjct: 190 AYAQK 194



 Score = 33.5 bits (75), Expect = 3e-05
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 329 LGLPKGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHT 388
           LG P G  + +D  GIDV     EE R+ +G D   P   +  + ++G+LG+K+  G + 
Sbjct: 518 LGFPMGQFAMSDLAGIDVGYRIREERRK-AGED--IPASWMDKLAEQGRLGQKTQAGVYK 574

Query: 389 YAHEEAK 395
           Y     K
Sbjct: 575 YEEGSRK 581


Lambda     K      H
   0.316    0.134    0.377 

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: 1001
Number of extensions: 51
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 702
Length adjustment: 39
Effective length of query: 612
Effective length of database: 663
Effective search space:   405756
Effective search space used:   405756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. 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 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