Alignments for a candidate for ech in Azospirillum sp. B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Azospirillum sp. B510

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 WP_148219526.1 AZL_RS21225 fatty acid oxidation complex subunit alpha FadB

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_000010725.1:WP_148219526.1
          Length = 721

 Score =  195 bits (496), Expect = 5e-54
 Identities = 129/401 (32%), Positives = 205/401 (51%), Gaps = 31/401 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60
           +  V+G+G+MG GIA  +A+ G  V M DI+   L   M +    L+K  E+G+L     
Sbjct: 313 RAAVLGAGIMGGGIAYQSAVCGIPVIMKDIAQSALDLGMTQAGALLAKRVETGALSSAKA 372

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           + +LA I P       +  +D ++EAV E++ +KR +    E H  P AV+ATNTSSL +
Sbjct: 373 DGILASIRPGLTY-DGIAEADVIVEAVVENIAIKRAVLAELEEHIRPDAVVATNTSSLLV 431

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           +++A  L+ P+  VGMHFFNP   MPLVE+++G  TS E V T    A +M K  +VV+D
Sbjct: 432 ADLARDLEWPENFVGMHFFNPVHRMPLVEVIQGPHTSPEAVATIVGYASAMGKTPVVVRD 491

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
            PGF VNR+L   +     L+  G A    +D +A+E  G+PMG   L D  G+D    V
Sbjct: 492 CPGFLVNRILAANVLGFLRLIHDG-ADFLRID-AAMEGFGWPMGPAWLQDVIGMDTSRHV 549

Query: 241 WKAVTA---RGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY-------------PSPGKFV 284
            + + A      +    ++ + +V   + G KSG+G+Y+Y             P  G  +
Sbjct: 550 IEVIAAGYPERMRVEFATALDVMVESKRFGQKSGAGFYRYEADAAGHQRKVVDPDVGALL 609

Query: 285 RPTLPSTSK-----KLGRYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLPK---GI 335
               P  S+     ++ +  + P + E +  L +G+VG   +A+   +LG+G P+   G 
Sbjct: 610 ATVQPGGSRIISDEEIVQRTMLPMILETARCLEDGVVGSAAEADMALILGIGFPRHLGGA 669

Query: 336 LSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEG 376
           L YADE+G   ++   +       +  Y P P +  +  +G
Sbjct: 670 LHYADELGAKTIMEWCDRYANLGPL--YHPTPRMRRLAVDG 708



 Score =  102 bits (255), Expect = 5e-26
 Identities = 66/178 (37%), Positives = 99/178 (55%), Gaps = 5/178 (2%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPV---KAMIAS 475
           N ++   + E+N+AL  + E   V  + IT     F  GAD+ EF  L  +   +  I +
Sbjct: 29  NKLDRLALDELNRALCLVREDRTVTGLLITSGKDSFIVGADIFEFTDLFGMAEDEIAIHN 88

Query: 476 RKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEINLGLIPGG 535
                V   +  L  P +  +NGLALGGG+ELAL+AD R+ S +A +G PE+ LG+ PG 
Sbjct: 89  AGQSAVITALADLPVPTVVAVNGLALGGGLELALAADVRMLSDSARIGLPEVGLGIFPGF 148

Query: 536 GGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL-ESEVRKLANAIA 591
           GGT RL RL G    L+ +++G   KA++A R G V+ +  P EL E+ + +L   +A
Sbjct: 149 GGTVRLPRLIGVEAALQWIMSGTPRKADDALRAGAVDAVVPPPELREAALERLHGLVA 206



 Score = 28.1 bits (61), Expect = 0.001
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 328 GLGLPKGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLS---MVKEGKLGRKSGQ 384
           G G P G     D IG+D   + +E +   +G           +   MV+  + G+KSG 
Sbjct: 527 GFGWPMGPAWLQDVIGMDTSRHVIEVI--AAGYPERMRVEFATALDVMVESKRFGQKSGA 584

Query: 385 GFHTYAHEEAKYSTIVV 401
           GF+ Y  + A +   VV
Sbjct: 585 GFYRYEADAAGHQRKVV 601


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: 930
Number of extensions: 50
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 721
Length adjustment: 39
Effective length of query: 612
Effective length of database: 682
Effective search space:   417384
Effective search space used:   417384
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 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