Alignments for a candidate for fadB in Azospirillum sp. B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Azospirillum sp. B510

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_148219526.1 AZL_RS21225 fatty acid oxidation complex subunit alpha FadB

Query= metacyc::MONOMER-17591
         (715 letters)



>NCBI__GCF_000010725.1:WP_148219526.1
          Length = 721

 Score =  700 bits (1806), Expect = 0.0
 Identities = 361/710 (50%), Positives = 481/710 (67%), Gaps = 3/710 (0%)

Query: 2   IYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTSG 61
           ++QG  + +  L  G+ EL FD  GESVNK +RL L EL  A+  ++ D +V G+++TSG
Sbjct: 1   MFQGNTLQLHALGDGLAELRFDRAGESVNKLDRLALDELNRALCLVREDRTVTGLLITSG 60

Query: 62  KDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLEM 121
           KD FIVGADI EF D F + ++E+   N   + + +   DL VPTV A+NG+ALGGGLE+
Sbjct: 61  KDSFIVGADIFEFTDLFGMAEDEIAIHNAGQSAVITALADLPVPTVVAVNGLALGGGLEL 120

Query: 122 CLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDALK 181
            LAAD R++S +A++GLPEV LGI+PGFGGTVRLPRLIG + A++WI SG   KA+DAL+
Sbjct: 121 ALAADVRMLSDSARIGLPEVGLGIFPGFGGTVRLPRLIGVEAALQWIMSGTPRKADDALR 180

Query: 182 VGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGFV 241
            GAVDAVV P +L+ AAL+     VA   D   RR+  L  + + A E +     A    
Sbjct: 181 AGAVDAVVPPPELREAALERLHGLVASP-DWSERRKEALSPV-VRAGEDLAPIFAAAKAK 238

Query: 242 AGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQELK 301
           A + GP+ PA +  ++ I+ AA   RD AL +EA  F  +A+T  A++L+ +F+NDQ +K
Sbjct: 239 ARKTGPHLPASLAVVELIESAAGVDRDAALALEARAFAHIARTPAARALVAVFINDQAVK 298

Query: 302 KKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKLL 361
           K  K+    A+ V  AAVLGAGIMGGGIAYQSA+ G P++MKDI +  + +G+ +A  LL
Sbjct: 299 KTTKQQTRAARPVSRAAVLGAGIMGGGIAYQSAVCGIPVIMKDIAQSALDLGMTQAGALL 358

Query: 362 GKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVKE 421
            KRVE G L+ AK    L  IRP ++Y      D++VEAVVEN  +K+AVLAE+E  ++ 
Sbjct: 359 AKRVETGALSSAKADGILASIRPGLTYDGIAEADVIVEAVVENIAIKRAVLAELEEHIRP 418

Query: 422 DAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVAY 481
           DA++A+NTS++ ++ LA+ L+ PENF GMHFFNPVH MPLVEVI+G  T   A+AT V Y
Sbjct: 419 DAVVATNTSSLLVADLARDLEWPENFVGMHFFNPVHRMPLVEVIQGPHTSPEAVATIVGY 478

Query: 482 AKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYLS 541
           A  MGK+P+VV DCPGFLVNR+L     GF +L+  G DF+RID  ME FGWPMGPA+L 
Sbjct: 479 ASAMGKTPVVVRDCPGFLVNRILAANVLGFLRLIHDGADFLRIDAAMEGFGWPMGPAWLQ 538

Query: 542 DVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGKPK 601
           DV+G+DT  H  +V+A G+P+RM VE  TA+DVM E+ R GQK+G GFY YE D  G  +
Sbjct: 539 DVIGMDTSRHVIEVIAAGYPERMRVEFATALDVMVESKRFGQKSGAGFYRYEADAAGHQR 598

Query: 602 KVTDPQAYEVLKPIVV-EQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIY 660
           KV DP    +L  +     R ++DE+IV   M+P+ LET RCLEDG+V +AAEADM LI 
Sbjct: 599 KVVDPDVGALLATVQPGGSRIISDEEIVQRTMLPMILETARCLEDGVVGSAAEADMALIL 658

Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNG 710
           GIGFP   GGAL Y D +G    +   D+YA LG LYHPT ++R +A +G
Sbjct: 659 GIGFPRHLGGALHYADELGAKTIMEWCDRYANLGPLYHPTPRMRRLAVDG 708


Lambda     K      H
   0.318    0.137    0.388 

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: 1182
Number of extensions: 51
Number of successful extensions: 3
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: 715
Length of database: 721
Length adjustment: 40
Effective length of query: 675
Effective length of database: 681
Effective search space:   459675
Effective search space used:   459675
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 (21.7 bits)
S2: 55 (25.8 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